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);
}
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}");
}
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);
}
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);
}
}
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);
}
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);
}
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);
}
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);
}