public void TestGetCountFingerprint()
{
Assert.IsTrue(trivialMol != null);
var circ = new CircularFingerprinter();
var result = circ.GetCountFingerprint(trivialMol);
int[] ANSWER_KEY = { -414937772, 1, -1027418143, 1, 1627608083, 1, -868007456, 1, -1006701866, 1,
-1059145289, 1, -801752141, 1, 790592664, 1, -289109509, 1, -1650154758, 1,1286833445, 1 };
int wantBits = ANSWER_KEY.Length >> 1;
bool fail = result.GetNumberOfPopulatedBins() != wantBits;
for (int n = 0; !fail && n < result.GetNumberOfPopulatedBins(); n++)
{
int gotHash = result.GetHash(n), gotCount = result.GetCount(n);
bool found = false;
for (int i = 0; i < wantBits; i++)
{
int wantHash = ANSWER_KEY[i * 2], wantCount = ANSWER_KEY[i * 2 + 1];
if (gotHash == wantHash)
{
found = true;
if (gotCount != wantCount)
{
throw new CDKException("For hash " + gotHash + " got count " + gotCount + " but wanted " + wantCount);
}
}
}
if (!found)
{
fail = true;
break;
}
}
if (fail)
{
throw new CDKException("Hash values do not match.");
}
}
/// <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();
}
