public virtual void TestGetAtomTypeFromJmol()
{
AtomTypeFactory factory = AtomTypeFactory.GetInstance("NCDK.Config.Data.jmol_atomtypes.txt");
IAtomType atomType = factory.GetAtomType("H");
Assert.IsNotNull(atomType);
Assert.AreEqual("H", atomType.Symbol);
Assert.AreEqual("H", atomType.AtomTypeName);
}
public virtual void TestGetAtomTypeFromPDB()
{
AtomTypeFactory factory = AtomTypeFactory.GetInstance("NCDK.Config.Data.pdb_atomtypes.xml");
IAtomType atomType = factory.GetAtomType("ALA.CA");
Assert.IsNotNull(atomType);
Assert.AreEqual("C", atomType.Symbol);
Assert.AreEqual("ALA.CA", atomType.AtomTypeName);
}
public virtual void TestGetAtomTypeFromOWL()
{
AtomTypeFactory factory = AtomTypeFactory.GetInstance("NCDK.Dict.Data.cdk-atom-types.owl");
IAtomType atomType;
atomType = factory.GetAtomType("C.sp3");
Assert.IsNotNull(atomType);
Assert.AreEqual("C", atomType.Symbol);
Assert.AreEqual("C.sp3", atomType.AtomTypeName);
Assert.AreEqual(Hybridization.SP3, atomType.Hybridization);
Assert.AreEqual(0, atomType.FormalCharge);
Assert.AreEqual(4, atomType.FormalNeighbourCount);
Assert.IsNotNull(atomType.GetProperty <object>(CDKPropertyName.LonePairCount));
Assert.AreEqual(0, atomType.GetProperty <int>(CDKPropertyName.LonePairCount));
Assert.AreEqual(0, atomType.GetProperty <int>(CDKPropertyName.PiBondCount));
Assert.AreEqual(BondOrder.Single, atomType.MaxBondOrder);
Assert.AreEqual(4.0, atomType.BondOrderSum.Value, 0.1);
atomType = factory.GetAtomType("N.sp2.radical");
Assert.IsNotNull(atomType);
Assert.AreEqual("N", atomType.Symbol);
Assert.AreEqual("N.sp2.radical", atomType.AtomTypeName);
Assert.AreEqual(Hybridization.SP2, atomType.Hybridization);
Assert.AreEqual(0, atomType.FormalCharge);
Assert.AreEqual(1, atomType.FormalNeighbourCount);
Assert.IsNotNull(atomType.GetProperty <object>(CDKPropertyName.LonePairCount));
Assert.AreEqual(1, atomType.GetProperty <int>(CDKPropertyName.LonePairCount));
Assert.AreEqual(1, atomType.GetProperty <int>(CDKPropertyName.PiBondCount));
Assert.AreEqual(BondOrder.Double, atomType.MaxBondOrder);
Assert.AreEqual(2.0, atomType.BondOrderSum.Value, 0.1);
atomType = factory.GetAtomType("N.planar3");
Assert.IsNotNull(atomType);
Assert.AreEqual("N", atomType.Symbol);
Assert.AreEqual("N.planar3", atomType.AtomTypeName);
Assert.AreEqual(Hybridization.Planar3, atomType.Hybridization);
Assert.AreEqual(0, atomType.FormalCharge);
Assert.AreEqual(3, atomType.FormalNeighbourCount);
Assert.IsNotNull(atomType.GetProperty <object>(CDKPropertyName.LonePairCount));
Assert.AreEqual(1, atomType.GetProperty <int>(CDKPropertyName.LonePairCount));
Assert.AreEqual(0, atomType.GetProperty <int>(CDKPropertyName.PiBondCount));
Assert.AreEqual(BondOrder.Single, atomType.MaxBondOrder);
Assert.AreEqual(3.0, atomType.BondOrderSum.Value, 0.1);
}
public virtual void TestGetAtomType_String()
{
var atomType = atf.GetAtomType("C4");
Assert.IsNotNull(atomType);
Assert.AreEqual("C", atomType.Symbol);
Assert.AreEqual("C4", atomType.AtomTypeName);
Assert.AreEqual(4.0, atomType.BondOrderSum ?? 0, 0.001);
Assert.AreEqual(BondOrder.Triple, atomType.MaxBondOrder);
}
public virtual void TestGetAtomTypeFromOWL_Sybyl()
{
AtomTypeFactory factory = AtomTypeFactory.GetInstance("NCDK.Dict.Data.sybyl-atom-types.owl");
IAtomType atomType;
atomType = factory.GetAtomType("C.3");
Assert.IsNotNull(atomType);
Assert.AreEqual("C", atomType.Symbol);
Assert.AreEqual("C.3", atomType.AtomTypeName);
Assert.AreEqual(4, atomType.FormalNeighbourCount);
Assert.AreEqual(Hybridization.SP3, atomType.Hybridization);
Assert.AreEqual(0, atomType.FormalCharge);
Assert.AreEqual(0, atomType.GetProperty <int?>(CDKPropertyName.LonePairCount));
Assert.AreEqual(0, atomType.GetProperty <int?>(CDKPropertyName.PiBondCount));
}
