m.addAtom(atom("O", 1, 0.00d, 2.48d)); m.addAtom(atom("C", 2, 0.71d, 2.06d)); m.addAtom(atom("C", 1, 0.71d, 1.24d)); m.addAtom(atom("O", 0, 1.43d, 0.82d)); m.addAtom(atom("C", 1, 1.43d, -0.00d)); m.addAtom(atom("O", 1, 2.14d, -0.41d)); m.addAtom(atom("C", 1, 0.71d, -0.41d)); m.addAtom(atom("O", 1, 0.71d, -1.24d)); m.addAtom(atom("C", 1, -0.00d, 0.00d)); m.addAtom(atom("O", 1, -0.71d, -0.41d)); m.addAtom(atom("C", 1, 0.00d, 0.83d)); m.addAtom(atom("O", 1, -0.71d, 1.24d)); m.addBond(0, 1, IBond.Order.SINGLE); m.addBond(2, 1, IBond.Order.SINGLE);
m.addAtom(atom("C", 1, 4.16d, 1.66d)); m.addAtom(atom("C", 1, 3.75d, 0.94d)); m.addAtom(atom("C", 1, 4.16d, 0.23d)); m.addAtom(atom("C", 1, 5.05d, 0.23d)); m.addAtom(atom("C", 1, 5.46d, 0.94d)); m.addAtom(atom("O", 0, 5.05d, 1.66d)); m.addAtom(atom("O", 1, 5.46d, 1.77d)); m.addAtom(atom("C", 2, 4.16d, 2.48d)); m.addAtom(atom("O", 1, 3.45d, 2.89d)); m.addAtom(atom("O", 1, 3.75d, 0.12d)); m.addAtom(atom("O", 1, 4.16d, 1.05d)); m.addAtom(atom("O", 1, 5.05d, -0.60d)); m.addBond(0, 1, IBond.Order.SINGLE); m.addBond(1, 2, IBond.Order.SINGLE); assertTetrahedralCenter(elements.get(0), m.getAtom(1), ITetrahedralChirality.Stereo.ANTI_CLOCKWISE, m.getAtom(1), m.getAtom(0), m.getAtom(9), m.getAtom(2)); assertTetrahedralCenter(elements.get(1), m.getAtom(2), ITetrahedralChirality.Stereo.ANTI_CLOCKWISE, m.getAtom(10), m.getAtom(1), m.getAtom(2), m.getAtom(3)); assertTetrahedralCenter(elements.get(2), m.getAtom(3), ITetrahedralChirality.Stereo.ANTI_CLOCKWISE, m.getAtom(3), m.getAtom(2), m.getAtom(11), m.getAtom(4)); assertTetrahedralCenter(elements.get(3), m.getAtom(4),
m.addAtom(atom("C", 1, -0.77d, 10.34d)); m.addAtom(atom("C", 1, 0.03d, 10.13d)); m.addAtom(atom("O", 0, 0.83d, 10.34d)); m.addAtom(atom("C", 1, 1.24d, 9.63d)); m.addAtom(atom("C", 1, 0.44d, 9.84d)); m.addAtom(atom("C", 1, -0.35d, 9.63d)); m.addAtom(atom("O", 1, 0.86d, 9.13d)); m.addAtom(atom("O", 1, 2.04d, 9.84d)); m.addAtom(atom("C", 2, -0.68d, 10.54d)); m.addAtom(atom("O", 1, -0.68d, 11.37d)); m.addAtom(atom("O", 1, -1.48d, 9.93d)); m.addAtom(atom("O", 1, -1.15d, 9.84d)); m.addBond(0, 1, IBond.Order.SINGLE); m.addBond(1, 2, IBond.Order.SINGLE); assertTetrahedralCenter(elements.get(0), m.getAtom(1), ITetrahedralChirality.Stereo.CLOCKWISE, m.getAtom(8), m.getAtom(0), m.getAtom(1), m.getAtom(2)); assertTetrahedralCenter(elements.get(1), m.getAtom(3), ITetrahedralChirality.Stereo.CLOCKWISE, m.getAtom(7), m.getAtom(2), m.getAtom(3), m.getAtom(4)); assertTetrahedralCenter(elements.get(2), m.getAtom(4), ITetrahedralChirality.Stereo.CLOCKWISE, m.getAtom(4), m.getAtom(3), m.getAtom(6), m.getAtom(5)); assertTetrahedralCenter(elements.get(3), m.getAtom(5),
m.addAtom(atom("O", 0, 2.56d, -6.46d)); m.addAtom(atom("C", 1, 1.90d, -6.83d)); m.addAtom(atom("C", 1, 2.15d, -7.46d)); m.addAtom(atom("C", 1, 2.98d, -7.46d)); m.addAtom(atom("C", 1, 3.23d, -6.83d)); m.addAtom(atom("C", 2, 1.90d, -6.00d)); m.addAtom(atom("O", 0, 1.18d, -5.59d)); m.addAtom(atom("O", 1, 2.15d, -8.29d)); m.addAtom(atom("O", 1, 2.98d, -8.29d)); m.addAtom(atom("P", 0, 0.36d, -5.59d)); m.addAtom(atom("O", 0, -0.47d, -5.59d)); m.addAtom(atom("O", 0, 0.36d, -4.76d)); m.addAtom(atom("O", 1, 0.36d, -6.41d)); m.addAtom(atom("P", 0, -1.29d, -5.59d)); m.addAtom(atom("O", 0, -2.12d, -5.59d)); m.addAtom(atom("O", 0, -1.29d, -4.76d)); m.addAtom(atom("O", 1, -1.29d, -6.41d)); m.addAtom(atom("P", 0, -2.94d, -5.59d)); m.addAtom(atom("O", 1, -3.77d, -5.59d)); m.addAtom(atom("O", 0, -2.94d, -4.76d)); m.addAtom(atom("O", 1, -2.94d, -6.41d)); m.addAtom(atom("C", 0, 4.73d, -4.51d)); m.addAtom(atom("C", 0, 4.02d, -4.92d)); m.addAtom(atom("C", 0, 4.02d, -5.75d)); m.addAtom(atom("N", 0, 4.73d, -6.16d)); m.addAtom(atom("N", 0, 5.44d, -5.75d)); m.addAtom(atom("C", 1, 5.44d, -4.92d)); m.addAtom(atom("C", 1, 2.75d, -5.33d)); m.addAtom(atom("N", 0, 3.23d, -4.67d));
m.addAtom(atom("C", 2, -0.71d, 0.41d)); m.addAtom(atom("C", 2, 0.71d, -0.41d)); m.addAtom(atom("C", 2, 0.71d, 0.41d)); m.addAtom(atom("C", 2, -0.71d, -0.41d)); m.addAtom(atom("C", 1, 0.00d, 0.82d)); m.addAtom(atom("C", 3, 0.00d, 1.65d)); m.addAtom(atom("C", 3, -0.71d, -2.06d)); m.addAtom(atom("C", 1, -0.00d, -1.65d)); m.addAtom(atom("C", 3, 0.71d, -2.06d)); m.addAtom(atom("C", 1, -0.00d, -0.83d)); m.addBond(9, 3, IBond.Order.SINGLE); m.addBond(0, 3, IBond.Order.SINGLE);
m.addAtom(atom("C", 0, 4.16d, 1.66d)); m.addAtom(atom("C", 0, 3.75d, 0.94d)); m.addAtom(atom("C", 0, 4.16d, 0.23d)); m.addAtom(atom("C", 0, 5.05d, 0.23d)); m.addAtom(atom("C", 0, 5.46d, 0.94d)); m.addAtom(atom("O", 0, 5.05d, 1.66d)); m.addAtom(atom("O", 1, 5.46d, 1.48d)); m.addAtom(atom("C", 2, 4.16d, 2.20d)); m.addAtom(atom("O", 1, 3.45d, 2.61d)); m.addAtom(atom("O", 1, 3.74d, 0.50d)); m.addAtom(atom("O", 1, 4.16d, 0.77d)); m.addAtom(atom("O", 1, 5.04d, -0.21d)); m.addAtom(atom("H", 0, 4.15d, -0.21d)); m.addAtom(atom("H", 0, 5.05d, 0.77d)); m.addAtom(atom("H", 0, 5.45d, 0.50d)); m.addAtom(atom("H", 0, 3.75d, 1.48d)); m.addAtom(atom("H", 0, 4.17d, 1.15d)); m.addBond(0, 1, IBond.Order.SINGLE); m.addBond(1, 2, IBond.Order.SINGLE); assertTetrahedralCenter(elements.get(0), m.getAtom(1), ITetrahedralChirality.Stereo.ANTI_CLOCKWISE, m.getAtom(15), m.getAtom(0), m.getAtom(9), m.getAtom(2)); assertTetrahedralCenter(elements.get(1), m.getAtom(2), ITetrahedralChirality.Stereo.ANTI_CLOCKWISE, m.getAtom(10), m.getAtom(1), m.getAtom(12), m.getAtom(3)); assertTetrahedralCenter(elements.get(2),
m.addAtom(atom("O", 0, -0.71d, 1.24d)); m.addAtom(atom("C", 0, 0.00d, 0.83d)); m.addAtom(atom("O", 0, 0.71d, 1.24d)); m.addAtom(atom("C", 1, 0.00d, 0.00d)); m.addAtom(atom("C", 2, -0.67d, -0.48d)); m.addAtom(atom("C", 2, -0.41d, -1.27d)); m.addAtom(atom("C", 2, 0.41d, -1.27d)); m.addAtom(atom("N", 1, 0.67d, -0.48d)); m.addBond(6, 5, IBond.Order.SINGLE); m.addBond(1, 0, IBond.Order.DOUBLE, IBond.Stereo.E_Z_BY_COORDINATES);
m.addAtom(atom("C", 1, 1.39d, 3.65d)); m.addAtom(atom("C", 2, 2.22d, 3.65d)); m.addAtom(atom("C", 1, 2.93d, 4.07d)); m.addAtom(atom("C", 1, 0.68d, 4.07d)); m.addAtom(atom("C", 1, 1.01d, 4.63d)); m.addAtom(atom("C", 1, 2.52d, 4.64d)); m.addAtom(atom("O", 0, 1.76d, 4.89d)); m.addAtom(atom("O", 1, 0.68d, 3.24d)); m.addAtom(atom("C", 2, 1.01d, 5.45d)); m.addAtom(atom("O", 1, 0.18d, 5.45d)); m.addAtom(atom("C", 3, 2.52d, 5.46d)); m.addAtom(atom("O", 0, 2.93d, 3.24d)); m.addAtom(atom("C", 2, 1.39d, 4.48d)); m.addAtom(atom("C", 3, 2.22d, 4.48d)); m.addAtom(atom("C", 2, 3.76d, 3.24d)); m.addAtom(atom("C", 2, 4.34d, 2.66d)); m.addAtom(atom("O", 0, 5.16d, 2.66d)); m.addAtom(atom("C", 3, 5.58d, 3.37d)); m.addBond(0, 1, IBond.Order.SINGLE); m.addBond(1, 2, IBond.Order.SINGLE); assertTetrahedralCenter(elements.get(0), m.getAtom(2), ITetrahedralChirality.Stereo.ANTI_CLOCKWISE, m.getAtom(2), m.getAtom(1), m.getAtom(11), m.getAtom(5)); assertTetrahedralCenter(elements.get(1), m.getAtom(5), ITetrahedralChirality.Stereo.ANTI_CLOCKWISE, m.getAtom(10), m.getAtom(2), m.getAtom(5), m.getAtom(6));
m.addAtom(atom("C", 1, -0.77d, 10.34d)); m.addAtom(atom("C", 1, 0.03d, 10.13d)); m.addAtom(atom("O", 0, 0.83d, 10.34d)); m.addAtom(atom("C", 1, 1.24d, 9.63d)); m.addAtom(atom("C", 1, 0.44d, 9.84d)); m.addAtom(atom("C", 1, -0.35d, 9.63d)); m.addAtom(atom("O", 1, 0.86d, 9.13d)); m.addAtom(atom("O", 1, 2.04d, 9.84d)); m.addAtom(atom("C", 2, -0.68d, 10.54d)); m.addAtom(atom("O", 1, -0.68d, 11.37d)); m.addAtom(atom("O", 1, -1.48d, 9.93d)); m.addAtom(atom("O", 1, -1.15d, 9.84d)); m.addBond(0, 1, IBond.Order.SINGLE); m.addBond(1, 2, IBond.Order.SINGLE); assertTetrahedralCenter(elements.get(0), m.getAtom(1), ITetrahedralChirality.Stereo.CLOCKWISE, m.getAtom(8), m.getAtom(0), m.getAtom(1), m.getAtom(2)); assertTetrahedralCenter(elements.get(1), m.getAtom(3), ITetrahedralChirality.Stereo.CLOCKWISE, m.getAtom(7), m.getAtom(2), m.getAtom(3), m.getAtom(4)); assertTetrahedralCenter(elements.get(2), m.getAtom(4), ITetrahedralChirality.Stereo.CLOCKWISE, m.getAtom(4), m.getAtom(3), m.getAtom(6), m.getAtom(5)); assertTetrahedralCenter(elements.get(3), m.getAtom(5),