test_class.declarator: smiles = new SmilesParser(SilentChemObjectBuilder.getInstance())
test_class.modifier: static
test_class.original_string: static SmilesParser   smiles = new SmilesParser(SilentChemObjectBuilder.getInstance());
test_class.type: SmilesParser
test_class.var_name: smiles
test_class.declarator: molecule
test_class.modifier: static
test_class.original_string: static IAtomContainer molecule;
test_class.type: IAtomContainer
test_class.var_name: molecule
test_class.declarator: ligands
test_class.modifier: static
test_class.original_string: static ILigand[]      ligands;
test_class.type: ILigand[]
test_class.var_name: ligands
test_class.file: descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/CIPToolTest.java
test_class.identifier: CIPToolTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testSteroid() {
          IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
          IAtomContainer mol = builder.newInstance(IAtomContainer.class);
          IAtom a1 = builder.newInstance(IAtom.class, "F");
          a1.setFormalCharge(0);
          a1.setPoint3d(new Point3d(7.0124, 2.5853, -0.9016));
          mol.addAtom(a1);
          IAtom a2 = builder.newInstance(IAtom.class, "O");
          a2.setFormalCharge(0);
          a2.setPoint3d(new Point3d(-0.5682, -0.2861, 2.1733));
          mol.addAtom(a2);
          IAtom a3 = builder.newInstance(IAtom.class, "O");
          a3.setFormalCharge(0);
          a3.setPoint3d(new Point3d(2.2826, -2.9598, -0.5754));
          mol.addAtom(a3);
          IAtom a4 = builder.newInstance(IAtom.class, "O");
          a4.setFormalCharge(0);
          a4.setPoint3d(new Point3d(-6.6808, -1.9515, 0.4596));
          mol.addAtom(a4);
          IAtom a5 = builder.newInstance(IAtom.class, "O");
          a5.setFormalCharge(0);
          a5.setPoint3d(new Point3d(4.2201, -1.7701, -1.7827));
          mol.addAtom(a5);
          IAtom a6 = builder.newInstance(IAtom.class, "O");
          a6.setFormalCharge(0);
          a6.setPoint3d(new Point3d(-7.0886, 0.761, 0.0885));
          mol.addAtom(a6);
          IAtom a7 = builder.newInstance(IAtom.class, "O");
          a7.setFormalCharge(0);
          a7.setPoint3d(new Point3d(-3.3025, 3.5973, -0.657));
          mol.addAtom(a7);
          IAtom a8 = builder.newInstance(IAtom.class, "C");
          a8.setFormalCharge(0);
          a8.setPoint3d(new Point3d(0.4862, -0.9146, 0.0574));
          mol.addAtom(a8);
          IAtom a9 = builder.newInstance(IAtom.class, "C");
          a9.setFormalCharge(0);
          a9.setPoint3d(new Point3d(-0.1943, 0.2177, 0.8706));
          mol.addAtom(a9);
          IAtom a10 = builder.newInstance(IAtom.class, "C");
          a10.setFormalCharge(0);
          a10.setPoint3d(new Point3d(1.7596, -1.1559, 0.9089));
          mol.addAtom(a10);
          IAtom a11 = builder.newInstance(IAtom.class, "C");
          a11.setFormalCharge(0);
          a11.setPoint3d(new Point3d(-2.4826, -0.4593, -0.073));
          mol.addAtom(a11);
          IAtom a12 = builder.newInstance(IAtom.class, "C");
          a12.setFormalCharge(0);
          a12.setPoint3d(new Point3d(-3.7166, 0.0102, -0.941));
          mol.addAtom(a12);
          IAtom a13 = builder.newInstance(IAtom.class, "C");
          a13.setFormalCharge(0);
          a13.setPoint3d(new Point3d(-0.4659, -2.1213, 0.0044));
          mol.addAtom(a13);
          IAtom a14 = builder.newInstance(IAtom.class, "C");
          a14.setFormalCharge(0);
          a14.setPoint3d(new Point3d(-1.485, 0.6715, 0.2231));
          mol.addAtom(a14);
          IAtom a15 = builder.newInstance(IAtom.class, "C");
          a15.setFormalCharge(0);
          a15.setPoint3d(new Point3d(0.9729, 1.1842, 1.122));
          mol.addAtom(a15);
          IAtom a16 = builder.newInstance(IAtom.class, "C");
          a16.setFormalCharge(0);
          a16.setPoint3d(new Point3d(2.1976, 0.2666, 1.3272));
          mol.addAtom(a16);
          IAtom a17 = builder.newInstance(IAtom.class, "C");
          a17.setFormalCharge(0);
          a17.setPoint3d(new Point3d(-1.8034, -1.7401, -0.6501));
          mol.addAtom(a17);
          IAtom a18 = builder.newInstance(IAtom.class, "C");
          a18.setFormalCharge(0);
          a18.setPoint3d(new Point3d(-4.2265, 1.3894, -0.4395));
          mol.addAtom(a18);
          IAtom a19 = builder.newInstance(IAtom.class, "C");
          a19.setFormalCharge(0);
          a19.setPoint3d(new Point3d(2.8802, -1.9484, 0.2485));
          mol.addAtom(a19);
          IAtom a20 = builder.newInstance(IAtom.class, "C");
          a20.setFormalCharge(0);
          a20.setPoint3d(new Point3d(0.862, -0.4809, -1.3862));
          mol.addAtom(a20);
          IAtom a21 = builder.newInstance(IAtom.class, "C");
          a21.setFormalCharge(0);
          a21.setPoint3d(new Point3d(-4.8907, -1.0078, -0.8633));
          mol.addAtom(a21);
          IAtom a22 = builder.newInstance(IAtom.class, "C");
          a22.setFormalCharge(0);
          a22.setPoint3d(new Point3d(-1.7576, 1.9697, 0.0241));
          mol.addAtom(a22);
          IAtom a23 = builder.newInstance(IAtom.class, "C");
          a23.setFormalCharge(0);
          a23.setPoint3d(new Point3d(-4.9064, 1.3293, 0.9405));
          mol.addAtom(a23);
          IAtom a24 = builder.newInstance(IAtom.class, "C");
          a24.setFormalCharge(0);
          a24.setPoint3d(new Point3d(-3.339, 0.1527, -2.4408));
          mol.addAtom(a24);
          IAtom a25 = builder.newInstance(IAtom.class, "C");
          a25.setFormalCharge(0);
          a25.setPoint3d(new Point3d(-3.1038, 2.4096, -0.4054));
          mol.addAtom(a25);
          IAtom a26 = builder.newInstance(IAtom.class, "C");
          a26.setFormalCharge(0);
          a26.setPoint3d(new Point3d(-5.5668, -1.0627, 0.5104));
          mol.addAtom(a26);
          IAtom a27 = builder.newInstance(IAtom.class, "C");
          a27.setFormalCharge(0);
          a27.setPoint3d(new Point3d(3.7564, -1.0338, -0.652));
          mol.addAtom(a27);
          IAtom a28 = builder.newInstance(IAtom.class, "C");
          a28.setFormalCharge(0);
          a28.setPoint3d(new Point3d(-6.0498, 0.3154, 0.9627));
          mol.addAtom(a28);
          IAtom a29 = builder.newInstance(IAtom.class, "C");
          a29.setFormalCharge(0);
          a29.setPoint3d(new Point3d(3.6914, -2.6828, 1.3258));
          mol.addAtom(a29);
          IAtom a30 = builder.newInstance(IAtom.class, "C");
          a30.setFormalCharge(0);
          a30.setPoint3d(new Point3d(4.9535, -0.3812, 0.0661));
          mol.addAtom(a30);
          IAtom a31 = builder.newInstance(IAtom.class, "C");
          a31.setFormalCharge(0);
          a31.setPoint3d(new Point3d(5.4727, 0.8461, -0.696));
          mol.addAtom(a31);
          IAtom a32 = builder.newInstance(IAtom.class, "C");
          a32.setFormalCharge(0);
          a32.setPoint3d(new Point3d(6.7079, 1.5265, -0.0844));
          mol.addAtom(a32);
          IAtom a33 = builder.newInstance(IAtom.class, "C");
          a33.setFormalCharge(0);
          a33.setPoint3d(new Point3d(6.4387, 2.104, 1.3013));
          mol.addAtom(a33);
          IAtom a34 = builder.newInstance(IAtom.class, "C");
          a34.setFormalCharge(0);
          a34.setPoint3d(new Point3d(7.9342, 0.6197, -0.0661));
          mol.addAtom(a34);
          IAtom a35 = builder.newInstance(IAtom.class, "H");
          a35.setFormalCharge(0);
          a35.setPoint3d(new Point3d(1.4474, -1.6941, 1.8161));
          mol.addAtom(a35);
          IAtom a36 = builder.newInstance(IAtom.class, "H");
          a36.setFormalCharge(0);
          a36.setPoint3d(new Point3d(-2.8575, -0.7521, 0.9166));
          mol.addAtom(a36);
          IAtom a37 = builder.newInstance(IAtom.class, "H");
          a37.setFormalCharge(0);
          a37.setPoint3d(new Point3d(-0.0529, -2.952, -0.5733));
          mol.addAtom(a37);
          IAtom a38 = builder.newInstance(IAtom.class, "H");
          a38.setFormalCharge(0);
          a38.setPoint3d(new Point3d(-0.6583, -2.5149, 1.01));
          mol.addAtom(a38);
          IAtom a39 = builder.newInstance(IAtom.class, "H");
          a39.setFormalCharge(0);
          a39.setPoint3d(new Point3d(1.1462, 1.8516, 0.2703));
          mol.addAtom(a39);
          IAtom a40 = builder.newInstance(IAtom.class, "H");
          a40.setFormalCharge(0);
          a40.setPoint3d(new Point3d(0.8186, 1.8095, 2.0087));
          mol.addAtom(a40);
          IAtom a41 = builder.newInstance(IAtom.class, "H");
          a41.setFormalCharge(0);
          a41.setPoint3d(new Point3d(2.5044, 0.2648, 2.3797));
          mol.addAtom(a41);
          IAtom a42 = builder.newInstance(IAtom.class, "H");
          a42.setFormalCharge(0);
          a42.setPoint3d(new Point3d(2.9822, 0.7582, 0.7671));
          mol.addAtom(a42);
          IAtom a43 = builder.newInstance(IAtom.class, "H");
          a43.setFormalCharge(0);
          a43.setPoint3d(new Point3d(-2.4854, -2.5906, -0.5319));
          mol.addAtom(a43);
          IAtom a44 = builder.newInstance(IAtom.class, "H");
          a44.setFormalCharge(0);
          a44.setPoint3d(new Point3d(-1.6353, -1.6475, -1.7261));
          mol.addAtom(a44);
          IAtom a45 = builder.newInstance(IAtom.class, "H");
          a45.setFormalCharge(0);
          a45.setPoint3d(new Point3d(-4.9616, 1.7691, -1.1638));
          mol.addAtom(a45);
          IAtom a46 = builder.newInstance(IAtom.class, "H");
          a46.setFormalCharge(0);
          a46.setPoint3d(new Point3d(-0.0354, -0.2446, -1.9684));
          mol.addAtom(a46);
          IAtom a47 = builder.newInstance(IAtom.class, "H");
          a47.setFormalCharge(0);
          a47.setPoint3d(new Point3d(1.3691, -1.2574, -1.9625));
          mol.addAtom(a47);
          IAtom a48 = builder.newInstance(IAtom.class, "H");
          a48.setFormalCharge(0);
          a48.setPoint3d(new Point3d(1.4296, 0.4511, -1.4252));
          mol.addAtom(a48);
          IAtom a49 = builder.newInstance(IAtom.class, "H");
          a49.setFormalCharge(0);
          a49.setPoint3d(new Point3d(-4.5596, -2.0138, -1.147));
          mol.addAtom(a49);
          IAtom a50 = builder.newInstance(IAtom.class, "H");
          a50.setFormalCharge(0);
          a50.setPoint3d(new Point3d(-5.6512, -0.7511, -1.6149));
          mol.addAtom(a50);
          IAtom a51 = builder.newInstance(IAtom.class, "H");
          a51.setFormalCharge(0);
          a51.setPoint3d(new Point3d(-1.0464, 2.7559, 0.2488));
          mol.addAtom(a51);
          IAtom a52 = builder.newInstance(IAtom.class, "H");
          a52.setFormalCharge(0);
          a52.setPoint3d(new Point3d(-4.1786, 1.0807, 1.7222));
          mol.addAtom(a52);
          IAtom a53 = builder.newInstance(IAtom.class, "H");
          a53.setFormalCharge(0);
          a53.setPoint3d(new Point3d(-5.2947, 2.3265, 1.1848));
          mol.addAtom(a53);
          IAtom a54 = builder.newInstance(IAtom.class, "H");
          a54.setFormalCharge(0);
          a54.setPoint3d(new Point3d(-2.421, 0.7311, -2.5838));
          mol.addAtom(a54);
          IAtom a55 = builder.newInstance(IAtom.class, "H");
          a55.setFormalCharge(0);
          a55.setPoint3d(new Point3d(-3.2008, -0.8224, -2.9194));
          mol.addAtom(a55);
          IAtom a56 = builder.newInstance(IAtom.class, "H");
          a56.setFormalCharge(0);
          a56.setPoint3d(new Point3d(-4.1353, 0.658, -3.0004));
          mol.addAtom(a56);
          IAtom a57 = builder.newInstance(IAtom.class, "H");
          a57.setFormalCharge(0);
          a57.setPoint3d(new Point3d(-4.8758, -1.4669, 1.2574));
          mol.addAtom(a57);
          IAtom a58 = builder.newInstance(IAtom.class, "H");
          a58.setFormalCharge(0);
          a58.setPoint3d(new Point3d(-0.9312, 0.4562, 2.6867));
          mol.addAtom(a58);
          IAtom a59 = builder.newInstance(IAtom.class, "H");
          a59.setFormalCharge(0);
          a59.setPoint3d(new Point3d(3.1882, -0.2287, -1.0977));
          mol.addAtom(a59);
          IAtom a60 = builder.newInstance(IAtom.class, "H");
          a60.setFormalCharge(0);
          a60.setPoint3d(new Point3d(-6.4869, 0.2469, 1.965));
          mol.addAtom(a60);
          IAtom a61 = builder.newInstance(IAtom.class, "H");
          a61.setFormalCharge(0);
          a61.setPoint3d(new Point3d(4.102, -2.0082, 2.0826));
          mol.addAtom(a61);
          IAtom a62 = builder.newInstance(IAtom.class, "H");
          a62.setFormalCharge(0);
          a62.setPoint3d(new Point3d(4.5162, -3.2434, 0.8708));
          mol.addAtom(a62);
          IAtom a63 = builder.newInstance(IAtom.class, "H");
          a63.setFormalCharge(0);
          a63.setPoint3d(new Point3d(3.0747, -3.4251, 1.8469));
          mol.addAtom(a63);
          IAtom a64 = builder.newInstance(IAtom.class, "H");
          a64.setFormalCharge(0);
          a64.setPoint3d(new Point3d(1.8961, -3.6368, 0.0058));
          mol.addAtom(a64);
          IAtom a65 = builder.newInstance(IAtom.class, "H");
          a65.setFormalCharge(0);
          a65.setPoint3d(new Point3d(5.7631, -1.1204, 0.1084));
          mol.addAtom(a65);
          IAtom a66 = builder.newInstance(IAtom.class, "H");
          a66.setFormalCharge(0);
          a66.setPoint3d(new Point3d(4.743, -0.1036, 1.1001));
          mol.addAtom(a66);
          IAtom a67 = builder.newInstance(IAtom.class, "H");
          a67.setFormalCharge(0);
          a67.setPoint3d(new Point3d(-6.3482, -2.8223, 0.1828));
          mol.addAtom(a67);
          IAtom a68 = builder.newInstance(IAtom.class, "H");
          a68.setFormalCharge(0);
          a68.setPoint3d(new Point3d(4.6594, -1.153, -2.3908));
          mol.addAtom(a68);
          IAtom a69 = builder.newInstance(IAtom.class, "H");
          a69.setFormalCharge(0);
          a69.setPoint3d(new Point3d(-7.3836, 1.6319, 0.4047));
          mol.addAtom(a69);
          IAtom a70 = builder.newInstance(IAtom.class, "H");
          a70.setFormalCharge(0);
          a70.setPoint3d(new Point3d(5.716, 0.5715, -1.7297));
          mol.addAtom(a70);
          IAtom a71 = builder.newInstance(IAtom.class, "H");
          a71.setFormalCharge(0);
          a71.setPoint3d(new Point3d(4.6721, 1.5926, -0.7787));
          mol.addAtom(a71);
          IBond b1 = builder.newInstance(IBond.class, a1, a32, IBond.Order.SINGLE);
          mol.addBond(b1);
          IBond b2 = builder.newInstance(IBond.class, a2, a9, IBond.Order.SINGLE);
          mol.addBond(b2);
          IBond b3 = builder.newInstance(IBond.class, a2, a58, IBond.Order.SINGLE);
          mol.addBond(b3);
          IBond b4 = builder.newInstance(IBond.class, a3, a19, IBond.Order.SINGLE);
          mol.addBond(b4);
          IBond b5 = builder.newInstance(IBond.class, a3, a64, IBond.Order.SINGLE);
          mol.addBond(b5);
          IBond b6 = builder.newInstance(IBond.class, a4, a26, IBond.Order.SINGLE);
          mol.addBond(b6);
          IBond b7 = builder.newInstance(IBond.class, a4, a67, IBond.Order.SINGLE);
          mol.addBond(b7);
          IBond b8 = builder.newInstance(IBond.class, a5, a27, IBond.Order.SINGLE);
          mol.addBond(b8);
          IBond b9 = builder.newInstance(IBond.class, a5, a68, IBond.Order.SINGLE);
          mol.addBond(b9);
          IBond b10 = builder.newInstance(IBond.class, a6, a28, IBond.Order.SINGLE);
          mol.addBond(b10);
          IBond b11 = builder.newInstance(IBond.class, a6, a69, IBond.Order.SINGLE);
          mol.addBond(b11);
          IBond b12 = builder.newInstance(IBond.class, a7, a25, IBond.Order.DOUBLE);
          mol.addBond(b12);
          IBond b13 = builder.newInstance(IBond.class, a8, a9, IBond.Order.SINGLE);
          mol.addBond(b13);
          IBond b14 = builder.newInstance(IBond.class, a8, a10, IBond.Order.SINGLE);
          mol.addBond(b14);
          IBond b15 = builder.newInstance(IBond.class, a8, a13, IBond.Order.SINGLE);
          mol.addBond(b15);
          IBond b16 = builder.newInstance(IBond.class, a8, a20, IBond.Order.SINGLE);
          mol.addBond(b16);
          IBond b17 = builder.newInstance(IBond.class, a9, a14, IBond.Order.SINGLE);
          mol.addBond(b17);
          IBond b18 = builder.newInstance(IBond.class, a9, a15, IBond.Order.SINGLE);
          mol.addBond(b18);
          IBond b19 = builder.newInstance(IBond.class, a10, a16, IBond.Order.SINGLE);
          mol.addBond(b19);
          IBond b20 = builder.newInstance(IBond.class, a10, a19, IBond.Order.SINGLE);
          mol.addBond(b20);
          IBond b21 = builder.newInstance(IBond.class, a10, a35, IBond.Order.SINGLE);
          mol.addBond(b21);
          IBond b22 = builder.newInstance(IBond.class, a11, a12, IBond.Order.SINGLE);
          mol.addBond(b22);
          IBond b23 = builder.newInstance(IBond.class, a11, a14, IBond.Order.SINGLE);
          mol.addBond(b23);
          IBond b24 = builder.newInstance(IBond.class, a11, a17, IBond.Order.SINGLE);
          mol.addBond(b24);
          IBond b25 = builder.newInstance(IBond.class, a11, a36, IBond.Order.SINGLE);
          mol.addBond(b25);
          IBond b26 = builder.newInstance(IBond.class, a12, a18, IBond.Order.SINGLE);
          mol.addBond(b26);
          IBond b27 = builder.newInstance(IBond.class, a12, a21, IBond.Order.SINGLE);
          mol.addBond(b27);
          IBond b28 = builder.newInstance(IBond.class, a12, a24, IBond.Order.SINGLE);
          mol.addBond(b28);
          IBond b29 = builder.newInstance(IBond.class, a13, a17, IBond.Order.SINGLE);
          mol.addBond(b29);
          IBond b30 = builder.newInstance(IBond.class, a13, a37, IBond.Order.SINGLE);
          mol.addBond(b30);
          IBond b31 = builder.newInstance(IBond.class, a13, a38, IBond.Order.SINGLE);
          mol.addBond(b31);
          IBond b32 = builder.newInstance(IBond.class, a14, a22, IBond.Order.DOUBLE);
          mol.addBond(b32);
          IBond b33 = builder.newInstance(IBond.class, a15, a16, IBond.Order.SINGLE);
          mol.addBond(b33);
          IBond b34 = builder.newInstance(IBond.class, a15, a39, IBond.Order.SINGLE);
          mol.addBond(b34);
          IBond b35 = builder.newInstance(IBond.class, a15, a40, IBond.Order.SINGLE);
          mol.addBond(b35);
          IBond b36 = builder.newInstance(IBond.class, a16, a41, IBond.Order.SINGLE);
          mol.addBond(b36);
          IBond b37 = builder.newInstance(IBond.class, a16, a42, IBond.Order.SINGLE);
          mol.addBond(b37);
          IBond b38 = builder.newInstance(IBond.class, a17, a43, IBond.Order.SINGLE);
          mol.addBond(b38);
          IBond b39 = builder.newInstance(IBond.class, a17, a44, IBond.Order.SINGLE);
          mol.addBond(b39);
          IBond b40 = builder.newInstance(IBond.class, a18, a23, IBond.Order.SINGLE);
          mol.addBond(b40);
          IBond b41 = builder.newInstance(IBond.class, a18, a25, IBond.Order.SINGLE);
          mol.addBond(b41);
          IBond b42 = builder.newInstance(IBond.class, a18, a45, IBond.Order.SINGLE);
          mol.addBond(b42);
          IBond b43 = builder.newInstance(IBond.class, a19, a27, IBond.Order.SINGLE);
          mol.addBond(b43);
          IBond b44 = builder.newInstance(IBond.class, a19, a29, IBond.Order.SINGLE);
          mol.addBond(b44);
          IBond b45 = builder.newInstance(IBond.class, a20, a46, IBond.Order.SINGLE);
          mol.addBond(b45);
          IBond b46 = builder.newInstance(IBond.class, a20, a47, IBond.Order.SINGLE);
          mol.addBond(b46);
          IBond b47 = builder.newInstance(IBond.class, a20, a48, IBond.Order.SINGLE);
          mol.addBond(b47);
          IBond b48 = builder.newInstance(IBond.class, a21, a26, IBond.Order.SINGLE);
          mol.addBond(b48);
          IBond b49 = builder.newInstance(IBond.class, a21, a49, IBond.Order.SINGLE);
          mol.addBond(b49);
          IBond b50 = builder.newInstance(IBond.class, a21, a50, IBond.Order.SINGLE);
          mol.addBond(b50);
          IBond b51 = builder.newInstance(IBond.class, a22, a25, IBond.Order.SINGLE);
          mol.addBond(b51);
          IBond b52 = builder.newInstance(IBond.class, a22, a51, IBond.Order.SINGLE);
          mol.addBond(b52);
          IBond b53 = builder.newInstance(IBond.class, a23, a28, IBond.Order.SINGLE);
          mol.addBond(b53);
          IBond b54 = builder.newInstance(IBond.class, a23, a52, IBond.Order.SINGLE);
          mol.addBond(b54);
          IBond b55 = builder.newInstance(IBond.class, a23, a53, IBond.Order.SINGLE);
          mol.addBond(b55);
          IBond b56 = builder.newInstance(IBond.class, a24, a54, IBond.Order.SINGLE);
          mol.addBond(b56);
          IBond b57 = builder.newInstance(IBond.class, a24, a55, IBond.Order.SINGLE);
          mol.addBond(b57);
          IBond b58 = builder.newInstance(IBond.class, a24, a56, IBond.Order.SINGLE);
          mol.addBond(b58);
          IBond b59 = builder.newInstance(IBond.class, a26, a28, IBond.Order.SINGLE);
          mol.addBond(b59);
          IBond b60 = builder.newInstance(IBond.class, a26, a57, IBond.Order.SINGLE);
          mol.addBond(b60);
          IBond b61 = builder.newInstance(IBond.class, a27, a30, IBond.Order.SINGLE);
          mol.addBond(b61);
          IBond b62 = builder.newInstance(IBond.class, a27, a59, IBond.Order.SINGLE);
          mol.addBond(b62);
          IBond b63 = builder.newInstance(IBond.class, a28, a60, IBond.Order.SINGLE);
          mol.addBond(b63);
          IBond b64 = builder.newInstance(IBond.class, a29, a61, IBond.Order.SINGLE);
          mol.addBond(b64);
          IBond b65 = builder.newInstance(IBond.class, a29, a62, IBond.Order.SINGLE);
          mol.addBond(b65);
          IBond b66 = builder.newInstance(IBond.class, a29, a63, IBond.Order.SINGLE);
          mol.addBond(b66);
          IBond b67 = builder.newInstance(IBond.class, a30, a31, IBond.Order.SINGLE);
          mol.addBond(b67);
          IBond b68 = builder.newInstance(IBond.class, a30, a65, IBond.Order.SINGLE);
          mol.addBond(b68);
          IBond b69 = builder.newInstance(IBond.class, a30, a66, IBond.Order.SINGLE);
          mol.addBond(b69);
          IBond b70 = builder.newInstance(IBond.class, a31, a32, IBond.Order.SINGLE);
          mol.addBond(b70);
          IBond b71 = builder.newInstance(IBond.class, a31, a70, IBond.Order.SINGLE);
          mol.addBond(b71);
          IBond b72 = builder.newInstance(IBond.class, a31, a71, IBond.Order.SINGLE);
          mol.addBond(b72);
          IBond b73 = builder.newInstance(IBond.class, a32, a33, IBond.Order.SINGLE);
          mol.addBond(b73);
          IBond b74 = builder.newInstance(IBond.class, a32, a34, IBond.Order.SINGLE);
          mol.addBond(b74);
  
          IAtom[] ligandAtoms = new IAtom[4];
          ligandAtoms[0] = a1; // F
          ligandAtoms[1] = a33; // Me
          ligandAtoms[2] = a34; // Me
          ligandAtoms[3] = a31; // rest of molecule
          Stereo stereo = StereoTool.getStereo(ligandAtoms[0], ligandAtoms[1], ligandAtoms[2], ligandAtoms[3]);
          ITetrahedralChirality tetraStereo = new TetrahedralChirality(a32, ligandAtoms, stereo);
  
          Assert.assertEquals(CIP_CHIRALITY.NONE, CIPTool.getCIPChirality(mol, tetraStereo));
      }
test_case.class_method_signature: CIPToolTest.testSteroid()
test_case.full_signature: @Test public void testSteroid()
test_case.identifier: testSteroid
test_case.invocations: getInstance newInstance newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance setFormalCharge setPoint3d addAtom newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond newInstance addBond getStereo assertEquals getCIPChirality
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testSteroid()
focal_class.declarator: HYDROGEN = -1
focal_class.modifier: public static final
focal_class.original_string: public static final int      HYDROGEN = -1;
focal_class.type: int
focal_class.var_name: HYDROGEN
focal_class.declarator: cipRule  = new CIPLigandRule()
focal_class.modifier: private static
focal_class.original_string: private static CIPLigandRule cipRule  = new CIPLigandRule();
focal_class.type: CIPLigandRule
focal_class.var_name: cipRule
focal_class.file: descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/CIPTool.java
focal_class.identifier: CIPTool
focal_class.class_method_signature: CIPTool.getCIPChirality(LigancyFourChirality stereoCenter)
focal_class.full_signature: public static CIP_CHIRALITY getCIPChirality(LigancyFourChirality stereoCenter)
focal_class.identifier: getCIPChirality
focal_class.modifiers: public static
focal_class.parameters: (LigancyFourChirality stereoCenter)
focal_class.return: CIP_CHIRALITY
focal_class.signature: CIP_CHIRALITY getCIPChirality(LigancyFourChirality stereoCenter)
focal_class.class_method_signature: CIPTool.label(IAtomContainer container)
focal_class.full_signature: public static void label(IAtomContainer container)
focal_class.identifier: label
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: void
focal_class.signature: void label(IAtomContainer container)
focal_class.class_method_signature: CIPTool.getCIPChirality(IAtomContainer container, ITetrahedralChirality stereoCenter)
focal_class.full_signature: public static CIP_CHIRALITY getCIPChirality(IAtomContainer container, ITetrahedralChirality stereoCenter)
focal_class.identifier: getCIPChirality
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, ITetrahedralChirality stereoCenter)
focal_class.return: CIP_CHIRALITY
focal_class.signature: CIP_CHIRALITY getCIPChirality(IAtomContainer container, ITetrahedralChirality stereoCenter)
focal_class.class_method_signature: CIPTool.getCIPChirality(IAtomContainer container, IDoubleBondStereochemistry stereoCenter)
focal_class.full_signature: public static CIP_CHIRALITY getCIPChirality(IAtomContainer container, IDoubleBondStereochemistry stereoCenter)
focal_class.identifier: getCIPChirality
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, IDoubleBondStereochemistry stereoCenter)
focal_class.return: CIP_CHIRALITY
focal_class.signature: CIP_CHIRALITY getCIPChirality(IAtomContainer container, IDoubleBondStereochemistry stereoCenter)
focal_class.class_method_signature: CIPTool.getLigands(IAtom atom, IAtomContainer container, IAtom exclude)
focal_class.full_signature: private static ILigand[] getLigands(IAtom atom, IAtomContainer container, IAtom exclude)
focal_class.identifier: getLigands
focal_class.modifiers: private static
focal_class.parameters: (IAtom atom, IAtomContainer container, IAtom exclude)
focal_class.return: ILigand[]
focal_class.signature: ILigand[] getLigands(IAtom atom, IAtomContainer container, IAtom exclude)
focal_class.class_method_signature: CIPTool.checkIfAllLigandsAreDifferent(ILigand[] ligands)
focal_class.full_signature: public static boolean checkIfAllLigandsAreDifferent(ILigand[] ligands)
focal_class.identifier: checkIfAllLigandsAreDifferent
focal_class.modifiers: public static
focal_class.parameters: (ILigand[] ligands)
focal_class.return: boolean
focal_class.signature: boolean checkIfAllLigandsAreDifferent(ILigand[] ligands)
focal_class.class_method_signature: CIPTool.order(ILigand[] ligands)
focal_class.full_signature: public static ILigand[] order(ILigand[] ligands)
focal_class.identifier: order
focal_class.modifiers: public static
focal_class.parameters: (ILigand[] ligands)
focal_class.return: ILigand[]
focal_class.signature: ILigand[] order(ILigand[] ligands)
focal_class.class_method_signature: CIPTool.permParity(final ILigand[] ligands)
focal_class.full_signature: private static int permParity(final ILigand[] ligands)
focal_class.identifier: permParity
focal_class.modifiers: private static
focal_class.parameters: (final ILigand[] ligands)
focal_class.return: int
focal_class.signature: int permParity(final ILigand[] ligands)
focal_class.class_method_signature: CIPTool.defineLigancyFourChirality(IAtomContainer container, int chiralAtom,
              int ligand1, int ligand2, int ligand3, int ligand4, Stereo stereo)
focal_class.full_signature: public static LigancyFourChirality defineLigancyFourChirality(IAtomContainer container, int chiralAtom,
              int ligand1, int ligand2, int ligand3, int ligand4, Stereo stereo)
focal_class.identifier: defineLigancyFourChirality
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, int chiralAtom,
              int ligand1, int ligand2, int ligand3, int ligand4, Stereo stereo)
focal_class.return: LigancyFourChirality
focal_class.signature: LigancyFourChirality defineLigancyFourChirality(IAtomContainer container, int chiralAtom,
              int ligand1, int ligand2, int ligand3, int ligand4, Stereo stereo)
focal_class.class_method_signature: CIPTool.defineLigand(IAtomContainer container, VisitedAtoms visitedAtoms, int chiralAtom,
              int ligandAtom)
focal_class.full_signature: public static ILigand defineLigand(IAtomContainer container, VisitedAtoms visitedAtoms, int chiralAtom,
              int ligandAtom)
focal_class.identifier: defineLigand
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, VisitedAtoms visitedAtoms, int chiralAtom,
              int ligandAtom)
focal_class.return: ILigand
focal_class.signature: ILigand defineLigand(IAtomContainer container, VisitedAtoms visitedAtoms, int chiralAtom,
              int ligandAtom)
focal_class.class_method_signature: CIPTool.getLigandLigands(ILigand ligand)
focal_class.full_signature: public static ILigand[] getLigandLigands(ILigand ligand)
focal_class.identifier: getLigandLigands
focal_class.modifiers: public static
focal_class.parameters: (ILigand ligand)
focal_class.return: ILigand[]
focal_class.signature: ILigand[] getLigandLigands(ILigand ligand)
focal_class.class_method_signature: CIPTool.getDuplication(Order order)
focal_class.full_signature: private static int getDuplication(Order order)
focal_class.identifier: getDuplication
focal_class.modifiers: private static
focal_class.parameters: (Order order)
focal_class.return: int
focal_class.signature: int getDuplication(Order order)
focal_method.body: public static CIP_CHIRALITY getCIPChirality(LigancyFourChirality stereoCenter) {
          ILigand[] ligands = order(stereoCenter.getLigands());
          LigancyFourChirality rsChirality = stereoCenter.project(ligands);
  
          boolean allAreDifferent = checkIfAllLigandsAreDifferent(ligands);
          if (!allAreDifferent) return CIP_CHIRALITY.NONE;
  
          if (rsChirality.getStereo() == Stereo.CLOCKWISE) return CIP_CHIRALITY.R;
  
          return CIP_CHIRALITY.S;
      }
focal_method.class_method_signature: CIPTool.getCIPChirality(LigancyFourChirality stereoCenter)
focal_method.full_signature: public static CIP_CHIRALITY getCIPChirality(LigancyFourChirality stereoCenter)
focal_method.identifier: getCIPChirality
focal_method.invocations: order getLigands project checkIfAllLigandsAreDifferent getStereo
focal_method.modifiers: public static
focal_method.parameters: (LigancyFourChirality stereoCenter)
focal_method.return: CIP_CHIRALITY
focal_method.signature: CIP_CHIRALITY getCIPChirality(LigancyFourChirality stereoCenter)