public void TestGetInstance_String_IChemObjectBuilder()
{
string configFile = "NCDK.Config.Data.structgen_atomtypes.xml";
AtomTypeFactory atf = AtomTypeFactory.GetInstance(configFile);
Assert.IsNotNull(atf);
Assert.AreNotSame(0, atf.Count);
}
public virtual void TestGetAllAtomTypes()
{
AtomTypeFactory atf = AtomTypeFactory.GetInstance();
IAtomType[] types = atf.GetAllAtomTypes()?.ToArray();
Assert.IsNotNull(types);
Assert.AreNotSame(0, types.Length);
}
public virtual void TestGetInstance_InputStream_String_IChemObjectBuilder()
{
var configFile = "NCDK.Config.Data.structgen_atomtypes.xml";
var ins = ResourceLoader.GetAsStream(typeof(AtomTypeFactory), configFile);
AtomTypeFactory atf = AtomTypeFactory.GetInstance(ins, "xml");
Assert.IsNotNull(atf);
Assert.AreNotSame(0, atf.Count);
}
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 TestConfigure_IAtom()
{
IAtom atom = builder.NewAtom();
atom.AtomTypeName = "C.ar";
AtomTypeFactory factory = AtomTypeFactory.GetInstance("NCDK.Config.Data.mol2_atomtypes.xml");
IAtomType atomType = factory.Configure(atom);
Assert.IsNotNull(atomType);
Assert.AreEqual("C", atom.Symbol);
}
public void Main()
{
{
#region 1
AtomTypeFactory factory = AtomTypeFactory.GetInstance();
#endregion
}
{
#region 2
AtomTypeFactory factory = AtomTypeFactory.GetInstance("NCDK.Config.Data.jmol_atomtypes.txt");
#endregion
}
}
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));
}
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 TestGetAtomTypeFromMM2()
{
AtomTypeFactory factory;
factory = AtomTypeFactory.GetInstance("NCDK.Config.Data.mm2_atomtypes.xml");
IAtomType atomType = factory.GetAtomType("C");
Assert.IsNotNull(atomType);
Assert.AreEqual("C", atomType.Symbol);
Assert.AreEqual("C", atomType.AtomTypeName);
Assert.AreEqual("[CSP]-[0-4][-]?+;[A-Za-z\\+\\-&&[^=%]]{0,6}[(].*+",
atomType.GetProperty <string>(CDKPropertyName.SphericalMatcher));
Assert.AreEqual(Hybridization.SP3, atomType.Hybridization);
atomType = factory.GetAtomType("Sthi");
Assert.IsNotNull(atomType);
Assert.AreEqual("S", atomType.Symbol);
Assert.AreEqual("Sthi", atomType.AtomTypeName);
Assert.AreEqual("S-[2];[H]{0,3}+=C.*+", atomType.GetProperty <string>(CDKPropertyName.SphericalMatcher));
Assert.AreEqual(Hybridization.SP2, atomType.Hybridization);
Assert.IsTrue(atomType.IsHydrogenBondAcceptor);
Assert.AreEqual(5, atomType.GetProperty <int?>(CDKPropertyName.PartOfRingOfSize));
}
public XMLIsotopeFactoryTest()
{
atf = AtomTypeFactory.GetInstance();
}
public void TestGetInstance_IChemObjectBuilder()
{
AtomTypeFactory atf = AtomTypeFactory.GetInstance();
Assert.IsNotNull(atf);
}
public virtual void TestGetSize()
{
AtomTypeFactory atf = AtomTypeFactory.GetInstance();
Assert.AreNotSame(0, atf.Count);
}
