Esempio n. 1
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        public void TestCalculate_BitFingerprint()
        {
            IAtomContainer mol1       = TestMoleculeFactory.MakeIndole();
            IAtomContainer mol2       = TestMoleculeFactory.MakePyrrole();
            Fingerprinter  fp         = new Fingerprinter(1024, 8);
            double         similarity = Tanimoto.Calculate(fp.GetBitFingerprint(mol1), fp.GetBitFingerprint(mol2));

            Assert.AreEqual(0.3939, similarity, 0.01 * 2);
        }
        public void TestICountFingerprintComparison()
        {
            var mol1          = TestMoleculeFactory.MakeIndole();
            var mol2          = TestMoleculeFactory.MakeIndole();
            var fingerprinter = new SignatureFingerprinter();
            var fp1           = fingerprinter.GetCountFingerprint(mol1);
            var fp2           = fingerprinter.GetCountFingerprint(mol2);
            var tanimoto      = Tanimoto.Calculate(fp1, fp2);

            Assert.AreEqual(1.0, tanimoto, 0.001);
        }
Esempio n. 3
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        void Main()
        {
            IAtomContainer molecule1     = null;
            IAtomContainer molecule2     = null;
            Fingerprinter  fingerprinter = null;

            #region 1
            BitArray fingerprint1         = fingerprinter.GetBitFingerprint(molecule1).AsBitSet();
            BitArray fingerprint2         = fingerprinter.GetBitFingerprint(molecule2).AsBitSet();
            double   tanimoto_coefficient = Tanimoto.Calculate(fingerprint1, fingerprint2);
            #endregion
        }
        public void TestRawTanimotoBetween0and1()
        {
            var smilesParser  = CDK.SmilesParser;
            var mol1          = smilesParser.ParseSmiles("Cc1nc(C(=O)NC23CC4CC(CC(C4)C2)C3)c(C)n1C5CCCCC5");
            var mol2          = smilesParser.ParseSmiles("CS(=O)(=O)Nc1ccc(Cc2onc(n2)c3ccc(cc3)S(=O)(=O)Nc4ccc(CCNC[C@H](O)c5cccnc5)cc4)cc1");
            var fingerprinter = new SignatureFingerprinter(0);
            var fp1           = fingerprinter.GetRawFingerprint(mol1);
            var fp2           = fingerprinter.GetRawFingerprint(mol2);
            var tanimoto      = Tanimoto.Calculate(fp1, fp2);

            Assert.IsTrue(tanimoto > 0 && tanimoto < 1, $"Tanimoto expected to be between 0 and 1, was:{tanimoto}");
        }
Esempio n. 5
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        public void Method2()
        {
            ICountFingerprint fp1 = new IntArrayCountFingerprint(new Dictionary <string, int>()
            {
                { "A", 3 }
            });
            ICountFingerprint fp2 = new IntArrayCountFingerprint(new Dictionary <string, int>()
            {
                { "A", 4 }
            });

            Assert.AreEqual(0.75, Tanimoto.Method2(fp1, fp2), 0.001);
        }
        public void CompareCountFingerprintAndRawFingerprintTanimoto()
        {
            var mol1          = TestMoleculeFactory.Make123Triazole();
            var mol2          = TestMoleculeFactory.MakeImidazole();
            var fingerprinter = new SignatureFingerprinter(1);
            var countFp1      = fingerprinter.GetCountFingerprint(mol1);
            var countFp2      = fingerprinter.GetCountFingerprint(mol2);
            var feat1         = fingerprinter.GetRawFingerprint(mol1);
            var feat2         = fingerprinter.GetRawFingerprint(mol2);
            var rawTanimoto   = Tanimoto.Calculate(feat1, feat2);
            var countTanimoto = Tanimoto.Method1(countFp1, countFp2);

            Assert.AreEqual(rawTanimoto, countTanimoto, 0.001);
        }
Esempio n. 7
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        public void TestTanimoto3()
        {
            double[] f1       = { 1, 2, 3, 4, 5, 6, 7 };
            double[] f2       = { 1, 2, 3, 4, 5, 6, 7 };
            var      tanimoto = Tanimoto.Calculate(f1, f2);

            if (standAlone)
            {
                System.Console.Out.WriteLine("Tanimoto: " + tanimoto);
            }
            if (!standAlone)
            {
                Assert.AreEqual(1.0, tanimoto, 0.001);
            }
        }
Esempio n. 8
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        public void TestExactMatch()
        {
            IAtomContainer mol1 = TestMoleculeFactory.MakeIndole();
            IAtomContainer mol2 = TestMoleculeFactory.MakeIndole();

            AddImplicitHydrogens(mol1);
            AddImplicitHydrogens(mol2);
            var fingerprinter = new LingoFingerprinter();

            AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol1);
            AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol2);
            var feat1    = fingerprinter.GetRawFingerprint(mol1);
            var feat2    = fingerprinter.GetRawFingerprint(mol2);
            var tanimoto = Tanimoto.Calculate(feat1, feat2);

            Assert.AreEqual(1.0, tanimoto, 0.001);
        }
Esempio n. 9
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        public void TestTanimoto2()
        {
            IAtomContainer mol1          = TestMoleculeFactory.MakeIndole();
            IAtomContainer mol2          = TestMoleculeFactory.MakeIndole();
            Fingerprinter  fingerprinter = new Fingerprinter();
            BitArray       bs1           = fingerprinter.GetBitFingerprint(mol1).AsBitSet();
            BitArray       bs2           = fingerprinter.GetBitFingerprint(mol2).AsBitSet();
            var            tanimoto      = Tanimoto.Calculate(bs1, bs2);

            if (standAlone)
            {
                System.Console.Out.WriteLine("Tanimoto: " + tanimoto);
            }
            if (!standAlone)
            {
                Assert.AreEqual(1.0, tanimoto, 0.001);
            }
        }
        public void TestCompaRingBitFingerprintAndCountBehavingAsBit()
        {
            var mol1 = TestMoleculeFactory.Make123Triazole();
            var mol2 = TestMoleculeFactory.MakeImidazole();

            var fingerprinter          = new SignatureFingerprinter(1);
            ICountFingerprint countFp1 = fingerprinter.GetCountFingerprint(mol1);
            ICountFingerprint countFp2 = fingerprinter.GetCountFingerprint(mol2);

            countFp1.SetBehaveAsBitFingerprint(true);
            countFp2.SetBehaveAsBitFingerprint(true);
            var bitFp1         = fingerprinter.GetBitFingerprint(mol1);
            var bitFp2         = fingerprinter.GetBitFingerprint(mol2);
            var bitTanimoto    = Tanimoto.Calculate(bitFp1, bitFp2);
            var countTanimoto1 = Tanimoto.Method1(countFp1, countFp2);
            var countTanimoto2 = Tanimoto.Method2(countFp1, countFp2);

            Assert.AreEqual(countTanimoto1, countTanimoto2, 0.001);
            Assert.AreEqual(bitTanimoto, countTanimoto1, 0.001);
        }
Esempio n. 11
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        public void TestCompareBitSetandBitFingerprintTanimoto()
        {
            IAtomContainer mol1          = TestMoleculeFactory.Make123Triazole();
            IAtomContainer mol2          = TestMoleculeFactory.MakeImidazole();
            Fingerprinter  fingerprinter = new Fingerprinter(1024, 8);
            BitArray       bs1           = fingerprinter.GetBitFingerprint(mol1).AsBitSet();
            BitArray       bs2           = fingerprinter.GetBitFingerprint(mol2).AsBitSet();
            var            tanimoto      = Tanimoto.Calculate(bs1, bs2);

            BitSetFingerprint fp1 = new BitSetFingerprint(bs1);
            BitSetFingerprint fp2 = new BitSetFingerprint(bs2);

            double tanimoto2 = Tanimoto.Calculate(fp1, fp2);

            Assert.AreEqual(tanimoto, tanimoto2, 0.01);

            IntArrayFingerprint ifp1 = new IntArrayFingerprint(fp1);
            IntArrayFingerprint ifp2 = new IntArrayFingerprint(fp2);

            tanimoto2 = Tanimoto.Calculate(ifp1, ifp2);
            Assert.AreEqual(tanimoto, tanimoto2, 0.01);
        }
        public void TestCountMethod1and2()
        {
            ICountFingerprint fp1 = new IntArrayCountFingerprint(new Dictionary <string, int>()
            {
                { "A", 3 }
            });
            ICountFingerprint fp2 = new IntArrayCountFingerprint(new Dictionary <string, int>()
            {
                { "A", 4 }
            });

            Assert.AreEqual(0.923, Tanimoto.Method1(fp1, fp2), 0.001);
            Assert.AreEqual(0.75, Tanimoto.Method2(fp1, fp2), 0.001);

            var mol1          = TestMoleculeFactory.MakeIndole();
            var mol2          = TestMoleculeFactory.MakeIndole();
            var fingerprinter = new SignatureFingerprinter();

            fp1 = fingerprinter.GetCountFingerprint(mol1);
            fp2 = fingerprinter.GetCountFingerprint(mol2);
            Assert.AreEqual(1.0, Tanimoto.Method1(fp1, fp2), 0.001);
            Assert.AreEqual(1.0, Tanimoto.Method2(fp1, fp2), 0.001);
        }
Esempio n. 13
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        public void KeggR00258()
        {
            var           sp            = CDK.SmilesParser;
            string        smiles1       = "O=C(O)CCC(=O)C(=O)O";
            string        smiles2       = "O=C(O)C(N)CCC(=O)O";
            string        smiles3       = "O=C(O)C(N)C";
            string        smiles4       = "CC(=O)C(=O)O";
            var           molecule1     = sp.ParseSmiles(smiles1);
            var           molecule2     = sp.ParseSmiles(smiles2);
            var           molecule3     = sp.ParseSmiles(smiles3);
            var           molecule4     = sp.ParseSmiles(smiles4);
            Fingerprinter fingerprinter = new Fingerprinter(1024, 6);
            BitArray      bs1           = fingerprinter.GetBitFingerprint(molecule1).AsBitSet();
            BitArray      bs2           = fingerprinter.GetBitFingerprint(molecule2).AsBitSet();
            BitArray      bs3           = fingerprinter.GetBitFingerprint(molecule3).AsBitSet();
            BitArray      bs4           = fingerprinter.GetBitFingerprint(molecule4).AsBitSet();

            Assert.AreEqual(0.75, (double)Tanimoto.Calculate(bs1, bs2), 0.1);
            Assert.AreEqual(0.46, (double)Tanimoto.Calculate(bs1, bs3), 0.1);
            Assert.AreEqual(0.52, (double)Tanimoto.Calculate(bs1, bs4), 0.1);
            Assert.AreEqual(0.53, (double)Tanimoto.Calculate(bs2, bs3), 0.1);
            Assert.AreEqual(0.42, (double)Tanimoto.Calculate(bs2, bs4), 0.1);
            Assert.AreEqual(0.8, (double)Tanimoto.Calculate(bs3, bs4), 0.1);
        }