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 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 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 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 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);
}
