public void TestPyrrole_Silent() { var smiles = "c2ccc3n([H])c1ccccc1c3(c2)"; var sp = new SmilesParser(builder, false); var molecule = sp.ParseSmiles(smiles); AtomContainerManipulator.SetSingleOrDoubleFlags(molecule); AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule); molecule = dbst.FixAromaticBondOrders(molecule); Assert.IsNotNull(molecule); molecule = (IAtomContainer)AtomContainerManipulator.RemoveHydrogens(molecule); int doubleBondCount = 0; for (int i = 0; i < molecule.Bonds.Count; i++) { IBond bond = molecule.Bonds[i]; Assert.IsTrue(bond.IsAromatic); if (bond.Order == BondOrder.Double) { doubleBondCount++; } } Assert.AreEqual(6, doubleBondCount); }
static void Main() { { IAtomContainer container = null; IAtom atom1 = null; IAtom atom2 = null; #region 1 AtomContainerManipulator.ReplaceAtomByAtom(container, atom1, atom2); #endregion } #region SetSingleOrDoubleFlags SmilesParser parser = new SmilesParser(ChemObjectBuilder.Instance, false); IAtomContainer biphenyl = parser.ParseSmiles("c1cccc(c1)c1ccccc1"); AtomContainerManipulator.SetSingleOrDoubleFlags(biphenyl); #endregion }