public void TestGetSize()
{
IFingerprinter fingerprinter = new Fingerprinter(512);
Assert.IsNotNull(fingerprinter);
Assert.AreEqual(512, fingerprinter.Length);
}
public void TestGetSearchDepth()
{
Fingerprinter fingerprinter = new Fingerprinter(512, 3);
Assert.IsNotNull(fingerprinter);
Assert.AreEqual(3, fingerprinter.SearchDepth);
}
public void TestgetBitFingerprint_IAtomContainer()
{
Fingerprinter fingerprinter = new Fingerprinter();
var mol = TestMoleculeFactory.MakeIndole();
IBitFingerprint bs = fingerprinter.GetBitFingerprint(mol);
Assert.IsNotNull(bs);
Assert.AreEqual(fingerprinter.Length, bs.Length);
}
public void TestVersion()
{
Fingerprinter fpr = new Fingerprinter(1024, 7);
fpr.SetPathLimit(2000);
fpr.SetHashPseudoAtoms(true);
string expected = "CDK-Fingerprinter/" + CDK.Version + " searchDepth=7 pathLimit=2000 hashPseudoAtoms=" + true.ToString();
Assert.AreEqual(expected, fpr.GetVersionDescription());
}
public void Main()
{
{
#region
var molecule = new AtomContainer();
var fingerprinter = new Fingerprinter();
var fingerprint = fingerprinter.GetBitFingerprint(molecule);
Console.WriteLine(fingerprint.Length); // returns 1024 by default
#endregion
}
}
public void TestIsSubSet_BitSet_BitSet()
{
Fingerprinter fingerprinter = new Fingerprinter();
IAtomContainer mol = TestMoleculeFactory.MakeIndole();
BitArray bs = fingerprinter.GetBitFingerprint(mol).AsBitSet();
IAtomContainer frag1 = TestMoleculeFactory.MakePyrrole();
BitArray bs1 = fingerprinter.GetBitFingerprint(frag1).AsBitSet();
Assert.IsTrue(FingerprinterTool.IsSubset(bs, bs1));
}
public void TestBug2819557()
{
IAtomContainer butane = MakeButane();
IAtomContainer propylAmine = MakePropylAmine();
Fingerprinter fp = new Fingerprinter();
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 TestFingerprinterBitSetSize()
{
Fingerprinter fingerprinter = new Fingerprinter(1024, 7);
Assert.IsNotNull(fingerprinter);
var mol = TestMoleculeFactory.MakeIndole();
BitArray bs = fingerprinter.GetBitFingerprint(mol).AsBitSet();
Assert.AreEqual(994, BitArrays.GetLength(bs)); // highest set bit
Assert.AreEqual(1024, bs.Count); // actual bit set size
}
public void TestAtomPermutation2()
{
IAtomContainer pamine = TestMoleculeFactory.MakeCyclopentane();
Fingerprinter fp = new Fingerprinter();
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 TestAtomPermutation()
{
var pamine = MakePropylAmine();
var fp = new Fingerprinter();
var bs1 = fp.GetBitFingerprint(pamine);
var acp = new AtomContainerAtomPermutor(pamine);
while (acp.MoveNext())
{
var container = acp.Current;
var bs2 = fp.GetBitFingerprint(container);
Assert.IsTrue(bs1.Equals(bs2));
}
}
public void Main()
{
{
#region IsSubset
var mol = TestMoleculeFactory.MakeIndole();
var fingerprinter = new Fingerprinter();
var bs = fingerprinter.GetBitFingerprint(mol);
var frag1 = TestMoleculeFactory.MakePyrrole();
var bs1 = fingerprinter.GetBitFingerprint(frag1);
if (FingerprinterTool.IsSubset(bs.AsBitSet(), bs1.AsBitSet()))
{
Console.Out.WriteLine("Pyrrole is subset of Indole.");
}
#endregion
}
}
public void TestRegression()
{
IAtomContainer mol1 = TestMoleculeFactory.MakeIndole();
IAtomContainer mol2 = TestMoleculeFactory.MakePyrrole();
Fingerprinter fingerprinter = new Fingerprinter(1024, 8);
IBitFingerprint bs1 = fingerprinter.GetBitFingerprint(mol1);
Assert.AreEqual(
33, 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(
13, bs2.Cardinality,
"Seems the fingerprint code has changed. This will cause a number of other tests to fail too!");
}
public void Testbug2917084()
{
string filename1 = "NCDK.Data.MDL.boronBuckyBall.mol";
Trace.TraceInformation("Testing: " + filename1);
var ins1 = ResourceLoader.GetAsStream(filename1);
var reader = new MDLV2000Reader(ins1, ChemObjectReaderMode.Strict);
var chemFile = reader.Read(builder.NewChemFile());
Assert.IsNotNull(chemFile);
var mol = ChemFileManipulator.GetAllAtomContainers(chemFile).First();
Fingerprinter fingerprinter = new Fingerprinter(1024, 8);
Assert.IsNotNull(fingerprinter.GetBitFingerprint(mol));
}
public void TestBug1851202()
{
string filename1 = "NCDK.Data.MDL.0002.stg01.rxn";
Trace.TraceInformation("Testing: " + filename1);
var ins1 = ResourceLoader.GetAsStream(filename1);
MDLRXNV2000Reader reader = new MDLRXNV2000Reader(ins1, ChemObjectReaderMode.Strict);
IReaction reaction = (IReaction)reader.Read(builder.NewReaction());
Assert.IsNotNull(reaction);
IAtomContainer reactant = reaction.Reactants[0];
IAtomContainer product = reaction.Products[0];
Fingerprinter fingerprinter = new Fingerprinter(64 * 26, 8);
Assert.IsNotNull(fingerprinter.GetBitFingerprint(reactant));
Assert.IsNotNull(fingerprinter.GetBitFingerprint(product));
}
public void PseudoAtomFingerprintArom()
{
SmilesParser smipar = CDK.SmilesParser;
string query = "*1cnccc1";
string indole = "n1cnccc1";
var queryMol = smipar.ParseSmiles(query);
var indoleMol = smipar.ParseSmiles(indole);
Fingerprinter fpr = new Fingerprinter();
BitArray fp1 = fpr.GetFingerprint(queryMol);
BitArray fp2 = fpr.GetFingerprint(indoleMol);
Assert.IsTrue(FingerprinterTool.IsSubset(fp2, fp1));
Assert.IsFalse(FingerprinterTool.IsSubset(fp1, fp2));
fpr.SetHashPseudoAtoms(true);
BitArray fp3 = fpr.GetFingerprint(queryMol);
BitArray fp4 = fpr.GetFingerprint(indoleMol);
Assert.IsFalse(FingerprinterTool.IsSubset(fp4, fp3));
Assert.IsFalse(FingerprinterTool.IsSubset(fp3, fp4));
}
/// <summary>
/// Constructs a fingerprint generator that creates fingerprints of
/// the given size, using a generation algorithm with the given search
/// depth.
/// </summary>
/// <param name="size">The desired size of the fingerprint</param>
/// <param name="searchDepth">The desired depth of search</param>
public ExtendedFingerprinter(int size, int searchDepth)
{
this.fingerprinter = new Fingerprinter(size - ReservedBits, searchDepth);
}