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 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 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 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 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 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 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 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));
}
/// <summary>
/// Generates a fingerprint of the default size for the given
/// AtomContainer, using path and ring metrics. It contains the
/// informations from <see cref="Fingerprinter.GetBitFingerprint(IAtomContainer)"/> and bits which tell if the structure
/// has 0 rings, 1 or less rings, 2 or less rings ... 10 or less rings and
/// bits which tell if there is a fused ring system with 1,2...8 or more
/// rings in it. The RingSet used is passed via rs parameter. This must be
/// a smallesSetOfSmallestRings. The List must be a list of all ring
/// systems in the molecule.
/// </summary>
/// <param name="atomContainer">The AtomContainer for which a Fingerprint is generated</param>
/// <param name="ringSet">An SSSR RingSet of ac (if not available, use <see cref="GetBitFingerprint(IAtomContainer)"/>, which does the calculation)</param>
/// <param name="rslist">A list of all ring systems in ac</param>
/// <exception cref="CDKException">for example if input can not be cloned.</exception>
/// <returns>a BitArray representing the fingerprint</returns>
public IBitFingerprint GetBitFingerprint(IAtomContainer atomContainer, IRingSet ringSet, IEnumerable <IRingSet> rslist)
{
var container = (IAtomContainer)atomContainer.Clone();
var fingerprint = fingerprinter.GetBitFingerprint(container);
var size = this.Length;
var weight = MolecularFormulaManipulator.GetTotalNaturalAbundance(MolecularFormulaManipulator.GetMolecularFormula(container));
for (int i = 1; i < 11; i++)
{
if (weight > (100 * i))
{
fingerprint.Set(size - 26 + i); // 26 := RESERVED_BITS+1
}
}
if (ringSet == null)
{
ringSet = Cycles.FindSSSR(container).ToRingSet();
rslist = RingPartitioner.PartitionRings(ringSet);
}
for (int i = 0; i < 7; i++)
{
if (ringSet.Count > i)
{
fingerprint.Set(size - 15 + i); // 15 := RESERVED_BITS+1+10 mass bits
}
}
int maximumringsystemsize = 0;
foreach (var rs in rslist)
{
if (rs.Count > maximumringsystemsize)
{
maximumringsystemsize = rs.Count;
}
}
for (int i = 0; i < maximumringsystemsize && i < 9; i++)
{
fingerprint.Set(size - 8 + i - 3);
}
return(fingerprint);
}
