public void TestReadAtomTypes2()
{
var data = "<atomTypeList xmlns=\"http://www.xml-cml.org/schema/cml2/core\" "
+ " xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" "
+ " xsi:schemaLocation=\"http://www.xml-cml.org/schema/cml2/core ../../io/cml/data/cmlAll.xsd\""
+ " id=\"mol2\" title=\"MOL2 AtomTypes\"> "
+ " "
+ " <atomType id=\"C.3\" title=\"1\"> "
+ " <atom elementType=\"C\"/> "
+ " <scalar dataType=\"xsd:string\" dictRef=\"cdk:hybridization\">sp3</scalar> "
+ " </atomType> "
+ " <atomType id=\"C.2\" title=\"2\"> "
+ " <atom elementType=\"C\"/> "
+ " <scalar dataType=\"xsd:string\" dictRef=\"cdk:hybridization\">sp2</scalar> "
+ " </atomType> "
+ "</atomTypeList>";
var reader = new AtomTypeReader(new StringReader(data));
Assert.IsNotNull(reader);
var types = reader.ReadAtomTypes();
Assert.IsNotNull(types);
Assert.AreEqual(2, types.Count());
}
public void TestReadAtomTypes_CDK()
{
var data = "<atomTypeList xmlns=\"http://www.xml-cml.org/schema/cml2/core\" \n"
+ " xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" \n"
+ " xsi:schemaLocation=\"http://www.xml-cml.org/schema/cml2/core ../../io/cml/data/cmlAll.xsd\"\n"
+ " id=\"mol2\" title=\"MOL2 AtomTypes\"> \n"
+ " \n"
+ " <atomType id=\"C.sp\">\n" + " <atom elementType=\"C\" formalCharge=\"0\">\n"
+ " <scalar dataType=\"xsd:integer\" dictRef=\"cdk:formalNeighbourCount\">2</scalar>\n"
+ " <scalar dataType=\"xsd:integer\" dictRef=\"cdk:lonePairCount\">0</scalar>\n"
+ " <scalar dataType=\"xsd:integer\" dictRef=\"cdk:piBondCount\">2</scalar>\n" + " </atom>\n"
+ " <scalar dataType=\"xsd:string\" dictRef=\"cdk:hybridization\">sp1</scalar>\n"
+ " </atomType> "
+ "</atomTypeList>";
var reader = new AtomTypeReader(new StringReader(data));
Assert.IsNotNull(reader);
var types = reader.ReadAtomTypes().ToReadOnlyList();
Assert.IsNotNull(types);
Assert.AreEqual(1, types.Count);
object obj = types[0];
Assert.IsNotNull(obj);
Assert.IsTrue(obj is IAtomType);
var atomType = (IAtomType)obj;
Assert.AreEqual(0, atomType.FormalCharge.Value);
Assert.AreEqual(Hybridization.SP1, atomType.Hybridization);
Assert.AreEqual(0, atomType.GetProperty <int?>(CDKPropertyName.LonePairCount));
Assert.AreEqual(2, atomType.GetProperty <int?>(CDKPropertyName.PiBondCount));
}
public void TestReadAtomTypes_FF()
{
var data = "<atomTypeList xmlns=\"http://www.xml-cml.org/schema/cml2/core\" \n"
+ " xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" \n"
+ " xsi:schemaLocation=\"http://www.xml-cml.org/schema/cml2/core ../../io/cml/data/cmlAll.xsd\"\n"
+ " id=\"mol2\" title=\"MOL2 AtomTypes\"> \n"
+ " \n"
+ " <atomType id=\"C\">\n" + " <!-- for example in CC-->\n"
+ " <atom elementType=\"C\" formalCharge=\"0\">\n"
+ " <scalar dataType=\"xsd:double\" dictRef=\"cdk:maxBondOrder\">1.0</scalar>\n"
+ " <scalar dataType=\"xsd:double\" dictRef=\"cdk:bondOrderSum\">4.0</scalar>\n"
+ " <scalar dataType=\"xsd:integer\" dictRef=\"cdk:formalNeighbourCount\">4</scalar>\n"
+ " <scalar dataType=\"xsd:integer\" dictRef=\"cdk:valency\">4</scalar>\n"
+ " <scalar dataType=\"xsd:string\" dictRef=\"cdk:hybridization\">sp3</scalar>\n"
+ " <scalar dataType=\"xsd:string\" dictRef=\"cdk:DA\">-</scalar>\n"
+ " <scalar dataType=\"xsd:string\" dictRef=\"cdk:sphericalMatcher\">[CSP]-[0-4][-]?+;</scalar>\n"
+ " <scalar dataType=\"xsd:integer\" dictRef=\"cdk:ringSize\">3</scalar>\n"
+ " <scalar dataType=\"xsd:integer\" dictRef=\"cdk:ringConstant\">3</scalar>\n" + " </atom>\n"
+ " </atomType>\n" + "</atomTypeList>\n";
var reader = new AtomTypeReader(new StringReader(data));
Assert.IsNotNull(reader);
var types = reader.ReadAtomTypes().ToReadOnlyList();
Assert.IsNotNull(types);
Assert.AreEqual(1, types.Count);
object obj = types[0];
Assert.IsNotNull(obj);
Assert.IsTrue(obj is IAtomType);
var atomType = (IAtomType)obj;
Assert.AreEqual("[CSP]-[0-4][-]?+;", atomType.GetProperty <string>(CDKPropertyName.SphericalMatcher));
Assert.IsFalse(atomType.IsHydrogenBondAcceptor);
Assert.IsFalse(atomType.IsHydrogenBondDonor);
Assert.AreEqual(3, atomType.GetProperty <int?>(CDKPropertyName.PartOfRingOfSize));
Assert.AreEqual(3, atomType.GetProperty <int?>(CDKPropertyName.ChemicalGroupConstant));
}