예제 #1
0
        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));
        }
예제 #2
0
        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());
        }
예제 #3
0
        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));
        }
예제 #4
0
        public void TestAtomTypeReader_Reader()
        {
            var reader = new AtomTypeReader(new StringReader(""));

            Assert.IsNotNull(reader);
        }