public void TestGetBitFingerprint()
{
Assert.IsTrue(trivialMol != null);
var circ = new CircularFingerprinter();
var result = circ.GetBitFingerprint(trivialMol);
BitArray wantBits = new BitArray(0), gotBits = result.AsBitSet();
int[] REQUIRE_BITS = { 19, 152, 293, 340, 439, 480, 507, 726, 762, 947, 993 };
foreach (var b in REQUIRE_BITS)
{
BitArrays.SetValue(wantBits, b, true);
}
if (!BitArrays.Equals(wantBits, gotBits))
{
throw new CDKException("Got " + gotBits + ", wanted " + wantBits);
}
}
/// <summary>
/// BuildTest
/// </summary>
public static void BuildTest()
{
CircularFingerprinter cfp = null;
CircularFingerprinterClass FpClass = CircularFingerprinterClass.ECFP6; // FP diameter
int FpLen = 2048; // folded binary fp length
IAtomContainer mol, mol2;
//string molfile = FileUtil.ReadFile(@"C:\Download\CorpId-12345.mol");
//java.io.StringReader sr = new java.io.StringReader(molfile);
//if (Lex.Contains(molfile, "v2000"))
// cor = new MDLV2000Reader(sr);
//else
// cor = new MDLV3000Reader(sr);
//cor.setReaderMode(IChemObjectReader.Mode.RELAXED);
//ac = (IAtomContainer)cor.read(new AtomContainer());
//cor.close();
FpClass = CircularFingerprinterClass.ECFP4; // debug
cfp = new CircularFingerprinter(FpClass, FpLen);
StreamReader reader = new StreamReader(@"C:\Download\CorpId-12345.mol");
//FileReader FileReader = new FileReader(@"C:\Download\V3000 Mols.sdf");
EnumerableSDFReader rdr = new EnumerableSDFReader(reader.BaseStream, ChemObjectBuilder.Instance);
rdr.ReaderMode = ChemObjectReaderMode.Relaxed;
IEnumerator <IAtomContainer> cursor = rdr.GetEnumerator();
while (cursor.MoveNext())
{
mol = cursor.Current;
mol = CdkMol.GetLargestMoleculeFragment(mol);
ICountFingerprint cfp1 = cfp.GetCountFingerprint(mol); // get hash values and counts for each
cfp.Calculate(mol);
int fpCount = cfp.FPCount;
for (int fpi = 0; fpi < fpCount; fpi++) // gets
{
CircularFingerprint cfp2 = cfp.GetFP(fpi); // gets hash, iteration and lists of atoms (dups appear multiple times)
}
IBitFingerprint bfp = cfp.GetBitFingerprint(mol);
BitArray bs = bfp.AsBitSet();
int bsCard = bfp.Cardinality;
long bsSize = bfp.Length;
continue;
}
reader.Close();
return;
//java.io.StringReader sr = new java.io.StringReader(molfile);
//AtomContainer mol = new AtomContainer();
//mol.addAtom(new Atom("C"));
//mol.addAtom(new Atom("H"));
//mol.addAtom(new Atom("H"));
//mol.addAtom(new Atom("H"));
//mol.addAtom(new Atom("H"));
//mol.addBond(new Bond(mol.getAtom(0), mol.getAtom(1)));
//mol.addBond(new Bond(mol.getAtom(0), mol.getAtom(2)));
//mol.addBond(new Bond(mol.getAtom(0), mol.getAtom(3)));
//mol.addBond(new Bond(mol.getAtom(0), mol.getAtom(4)));
//FileReader FileReader = new FileReader(@"C:\Download\CorpId-12345.mol");
//MolReader mr = new MolReader(FileReader, DefaultChemObjectBuilder.getInstance());
//java.io.StringReader sr = new java.io.StringReader(molfile);
//IMol m = (IMol)mr.next();
//FileReader.close();
}