public void TestLargeRingSystem()
{
var smiles = "O=C1Oc6ccccc6(C(O)C1C5c2ccccc2CC(c3ccc(cc3)c4ccccc4)C5)";
var smilesParser = CDK.SmilesParser;
var molecule = smilesParser.ParseSmiles(smiles);
molecule = FixBondOrdersTool.KekuliseAromaticRings(molecule);
Assert.IsNotNull(molecule);
molecule = (IAtomContainer)AtomContainerManipulator.RemoveHydrogens(molecule);
Assert.AreEqual(34, molecule.Atoms.Count);
// we should have 14 double bonds
int doubleBondCount = 0;
for (int i = 0; i < molecule.Bonds.Count; i++)
{
IBond bond = molecule.Bonds[i];
if (bond.Order == BondOrder.Double)
{
doubleBondCount++;
}
}
Assert.AreEqual(13, doubleBondCount);
}
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 = FixBondOrdersTool.KekuliseAromaticRings(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);
}
public void TestLargeBioclipseUseCase()
{
var smiles = "COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56";
var smilesParser = CDK.SmilesParser;
var molecule = smilesParser.ParseSmiles(smiles);
molecule = FixBondOrdersTool.KekuliseAromaticRings(molecule);
Assert.IsNotNull(molecule);
molecule = (IAtomContainer)AtomContainerManipulator.RemoveHydrogens(molecule);
Assert.AreEqual(40, molecule.Atoms.Count);
// we should have 14 double bonds
int doubleBondCount = 0;
for (int i = 0; i < molecule.Bonds.Count; i++)
{
IBond bond = molecule.Bonds[i];
if (bond.Order == BondOrder.Double)
{
doubleBondCount++;
}
}
Assert.AreEqual(10, doubleBondCount);
}
public void TestAcyclic()
{
var smiles = "CCCCCCC";
var smilesParser = CDK.SmilesParser;
var molecule = smilesParser.ParseSmiles(smiles);
molecule = FixBondOrdersTool.KekuliseAromaticRings(molecule);
Assert.IsNotNull(molecule);
}
public void XtestPyrrole()
{
var enol = builder.NewAtomContainer();
// atom block
var atom1 = builder.NewAtom(ChemicalElement.C);
atom1.Hybridization = Hybridization.SP2;
var atom2 = builder.NewAtom(ChemicalElement.C);
atom2.Hybridization = Hybridization.SP2;
var atom3 = builder.NewAtom(ChemicalElement.C);
atom3.Hybridization = Hybridization.SP2;
var atom4 = builder.NewAtom(ChemicalElement.C);
atom4.Hybridization = Hybridization.SP2;
var atom5 = builder.NewAtom(ChemicalElement.N);
atom5.Hybridization = Hybridization.SP2;
atom5.ImplicitHydrogenCount = 1;
// bond block
var bond1 = builder.NewBond(atom1, atom2);
var bond2 = builder.NewBond(atom2, atom3);
var bond3 = builder.NewBond(atom3, atom4);
var bond4 = builder.NewBond(atom4, atom5);
var bond5 = builder.NewBond(atom5, atom1);
enol.Atoms.Add(atom1);
enol.Atoms.Add(atom2);
enol.Atoms.Add(atom3);
enol.Atoms.Add(atom4);
enol.Atoms.Add(atom5);
enol.Bonds.Add(bond1);
enol.Bonds.Add(bond2);
enol.Bonds.Add(bond3);
enol.Bonds.Add(bond4);
enol.Bonds.Add(bond5);
// perceive atom types
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(enol);
// now have the algorithm have a go at it
enol = FixBondOrdersTool.KekuliseAromaticRings(enol);
Assert.IsNotNull(enol);
//Assert.IsTrue(FixBondOrdersTool.IsOK(enol));
// now check whether it did the right thing
Assert.AreEqual(BondOrder.Double, enol.Bonds[0].Order);;
Assert.AreEqual(BondOrder.Single, enol.Bonds[1].Order);;
Assert.AreEqual(BondOrder.Double, enol.Bonds[2].Order);;
Assert.AreEqual(BondOrder.Single, enol.Bonds[3].Order);;
Assert.AreEqual(BondOrder.Single, enol.Bonds[4].Order);;
}
public void XtestBenzene()
{
var enol = builder.NewAtomContainer();
// atom block
var atom1 = builder.NewAtom(ChemicalElement.C);
atom1.Hybridization = Hybridization.SP2;
var atom2 = builder.NewAtom(ChemicalElement.C);
atom2.Hybridization = Hybridization.SP2;
var atom3 = builder.NewAtom(ChemicalElement.C);
atom3.Hybridization = Hybridization.SP2;
var atom4 = builder.NewAtom(ChemicalElement.C);
atom4.Hybridization = Hybridization.SP2;
var atom5 = builder.NewAtom(ChemicalElement.C);
atom5.Hybridization = Hybridization.SP2;
var atom6 = builder.NewAtom(ChemicalElement.C);
atom6.Hybridization = Hybridization.SP2;
// bond block
var bond1 = builder.NewBond(atom1, atom2);
var bond2 = builder.NewBond(atom2, atom3);
var bond3 = builder.NewBond(atom3, atom4);
var bond4 = builder.NewBond(atom4, atom5);
var bond5 = builder.NewBond(atom5, atom6);
var bond6 = builder.NewBond(atom6, atom1);
enol.Atoms.Add(atom1);
enol.Atoms.Add(atom2);
enol.Atoms.Add(atom3);
enol.Atoms.Add(atom4);
enol.Atoms.Add(atom5);
enol.Atoms.Add(atom6);
enol.Bonds.Add(bond1);
enol.Bonds.Add(bond2);
enol.Bonds.Add(bond3);
enol.Bonds.Add(bond4);
enol.Bonds.Add(bond5);
enol.Bonds.Add(bond6);
// perceive atom types
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(enol);
// now have the algorithm have a go at it
enol = FixBondOrdersTool.KekuliseAromaticRings(enol);
Assert.IsNotNull(enol);
//Assert.IsTrue(dbst.IsOK(enol));
// now check whether it did the right thing
Assert.AreEqual(BondOrder.Single.Numeric() + BondOrder.Double.Numeric(), enol
.Bonds[0].Order.Numeric()
+ enol.Bonds[5].Order.Numeric()); // around atom1
Assert.AreEqual(BondOrder.Single.Numeric() + BondOrder.Double.Numeric(), enol
.Bonds[0].Order.Numeric()
+ enol.Bonds[1].Order.Numeric()); // around atom2
Assert.AreEqual(BondOrder.Single.Numeric() + BondOrder.Double.Numeric(), enol
.Bonds[1].Order.Numeric()
+ enol.Bonds[2].Order.Numeric()); // around atom3
Assert.AreEqual(BondOrder.Single.Numeric() + BondOrder.Double.Numeric(), enol
.Bonds[2].Order.Numeric()
+ enol.Bonds[3].Order.Numeric()); // around atom4
Assert.AreEqual(BondOrder.Single.Numeric() + BondOrder.Double.Numeric(), enol
.Bonds[3].Order.Numeric()
+ enol.Bonds[4].Order.Numeric()); // around atom5
Assert.AreEqual(BondOrder.Single.Numeric() + BondOrder.Double.Numeric(), enol
.Bonds[4].Order.Numeric()
+ enol.Bonds[5].Order.Numeric()); // around atom6
}