public void TestGetSize()
{
IFingerprinter fingerprinter = new ShortestPathFingerprinter(512);
Assert.IsNotNull(fingerprinter);
Assert.AreEqual(512, fingerprinter.Length);
}
public void TestBug2819557()
{
IAtomContainer butane = MakeButane();
IAtomContainer propylAmine = MakePropylAmine();
ShortestPathFingerprinter fp = new ShortestPathFingerprinter();
BitArray b1 = fp.GetBitFingerprint(butane).AsBitSet();
BitArray b2 = fp.GetBitFingerprint(propylAmine).AsBitSet();
Assert.IsFalse(FingerprinterTool.IsSubset(b2, b1), "butane should not be a substructure of propylamine");
}
public void Main()
{
{
#region
var molecule = new AtomContainer();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
var fingerprinter = new ShortestPathFingerprinter();
var fingerprint = fingerprinter.GetBitFingerprint(molecule);
Console.WriteLine(fingerprint.Length); // returns 1024 by default
#endregion
}
}
public void TestgetBitFingerprint_IAtomContainer()
{
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter();
IAtomContainer mol = TestMoleculeFactory.MakeIndole();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
IBitFingerprint bs = fingerprinter.GetBitFingerprint(mol);
Assert.IsNotNull(bs);
Assert.AreEqual(fingerprinter.Length, bs.Length);
}
public void TestFingerprinterBitSetSize()
{
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter(1024);
Assert.IsNotNull(fingerprinter);
IAtomContainer mol = TestMoleculeFactory.MakeIndole();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
BitArray bs = fingerprinter.GetBitFingerprint(mol).AsBitSet();
Assert.AreEqual(1024, bs.Length); // highest set bit
Assert.AreEqual(1024, bs.Count); // actual bit set size
}
public void TestGenerateFingerprintNaphthalene()
{
var smiles = "C1=CC2=CC=CC=C2C=C1";
var smilesParser = CDK.SmilesParser;
var molecule = smilesParser.ParseSmiles(smiles);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
Aromaticity.CDKLegacy.Apply(molecule);
ShortestPathFingerprinter fingerprint = new ShortestPathFingerprinter(1024);
BitArray fingerprint1;
fingerprint1 = fingerprint.GetBitFingerprint(molecule).AsBitSet();
Assert.AreEqual(8, BitArrays.Cardinality(fingerprint1));
}
public void TestRegression()
{
IAtomContainer mol1 = TestMoleculeFactory.MakeIndole();
IAtomContainer mol2 = TestMoleculeFactory.MakePyrrole();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol2);
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter();
IBitFingerprint bs1 = fingerprinter.GetBitFingerprint(mol1);
Assert.AreEqual(22, bs1.Cardinality, "Seems the fingerprint code has changed. This will cause a number of other tests to fail too!");
IBitFingerprint bs2 = fingerprinter.GetBitFingerprint(mol2);
Assert.AreEqual(11, bs2.Cardinality, "Seems the fingerprint code has changed. This will cause a number of other tests to fail too!");
}
public void TestAtomPermutation()
{
IAtomContainer pamine = MakePropylAmine();
ShortestPathFingerprinter fp = new ShortestPathFingerprinter();
IBitFingerprint bs1 = fp.GetBitFingerprint(pamine);
AtomContainerAtomPermutor acp = new AtomContainerAtomPermutor(pamine);
while (acp.MoveNext())
{
IAtomContainer container = acp.Current;
IBitFingerprint bs2 = fp.GetBitFingerprint(container);
Assert.IsTrue(bs1.Equals(bs2));
}
}
public void TestGenerateFingerprintMultiphtalene()
{
var smiles = "C1=CC2=CC=C3C4=CC5=CC6=CC=CC=C6C=C5C=C4C=CC3=C2C=C1";
var smilesParser = CDK.SmilesParser;
var molecule = smilesParser.ParseSmiles(smiles);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
ShortestPathFingerprinter fingerprint = new ShortestPathFingerprinter(1024);
BitArray fingerprint1;
fingerprint1 = fingerprint.GetBitFingerprint(molecule).AsBitSet();
Assert.AreEqual(15, BitArrays.Cardinality(fingerprint1));
}
public void TestAtomPermutation2()
{
IAtomContainer pamine = TestMoleculeFactory.MakeCyclopentane();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(pamine);
ShortestPathFingerprinter fp = new ShortestPathFingerprinter();
IBitFingerprint bs1 = fp.GetBitFingerprint(pamine);
AtomContainerAtomPermutor acp = new AtomContainerAtomPermutor(pamine);
while (acp.MoveNext())
{
IAtomContainer container = acp.Current;
IBitFingerprint bs2 = fp.GetBitFingerprint(container);
Assert.IsTrue(bs1.Equals(bs2));
}
}
public void TestFingerprinter_int_int()
{
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter(1024);
Assert.IsNotNull(fingerprinter);
IAtomContainer mol = TestMoleculeFactory.MakeIndole();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
BitArray bs = fingerprinter.GetBitFingerprint(mol).AsBitSet();
IAtomContainer frag1 = TestMoleculeFactory.MakePyrrole();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(frag1);
BitArray bs1 = fingerprinter.GetBitFingerprint(frag1).AsBitSet();
Assert.IsTrue(FingerprinterTool.IsSubset(bs, bs1));
}
public void TestGenerateFingerprintIsNotASubSet1()
{
string smilesT = "O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@@H]1O";
string smilesQ = "OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(O)=O";
var smilesParser = new SmilesParser(builder, false);
var moleculeQ = smilesParser.ParseSmiles(smilesQ);
var moleculeT = smilesParser.ParseSmiles(smilesT);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(moleculeQ);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(moleculeT);
ShortestPathFingerprinter fingerprint = new ShortestPathFingerprinter(1024);
BitArray fingerprintQ;
BitArray fingerprintT;
fingerprintQ = fingerprint.GetBitFingerprint(moleculeQ).AsBitSet();
fingerprintT = fingerprint.GetBitFingerprint(moleculeT).AsBitSet();
Assert.IsFalse(FingerprinterTool.IsSubset(fingerprintT, fingerprintQ));
}
public void TestGenerateFingerprintIsSubset()
{
string smilesT = "NC(=O)C1=C2C=CC(Br)=CC2=C(Cl)C=C1";
string smilesQ = "CC1=C2C=CC(Br)=CC2=C(Cl)C=C1";
var smilesParser = CDK.SmilesParser;
var moleculeQ = smilesParser.ParseSmiles(smilesQ);
var moleculeT = smilesParser.ParseSmiles(smilesT);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(moleculeQ);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(moleculeT);
ShortestPathFingerprinter fingerprint = new ShortestPathFingerprinter(1024);
BitArray fingerprintQ;
BitArray fingerprintT;
fingerprintQ = fingerprint.GetBitFingerprint(moleculeQ).AsBitSet();
fingerprintT = fingerprint.GetBitFingerprint(moleculeT).AsBitSet();
Assert.IsTrue(FingerprinterTool.IsSubset(fingerprintT, fingerprintQ));
}
