public static string CircularFpToString(CircularFingerprinter cfp)
{
CircularFingerprinter.FP fp = null;
string s = "fp\thashCode\titeration\tatoms\r\n";
int fpCount = cfp.getFPCount();
for (int fpi = 0; fpi < fpCount; fpi++)
{
fp = cfp.getFP(fpi);
s += fpi.ToString() + "\t" + fp.hashCode + "\t" + fp.iteration + "\t(" + string.Join(", ", fp.atoms) + ")\r\n";
}
return(s);
}
/// <summary>
/// BuildTest
/// </summary>
public static void BuildTest()
{
CircularFingerprinter cfp = null;
int FpClass = CircularFingerprinter.CLASS_ECFP6; // FP diameter
int FpLen = 2048; // folded binary fp length
DefaultChemObjectReader cor;
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 = CircularFingerprinter.CLASS_ECFP4; // debug
cfp = new CircularFingerprinter(FpClass, FpLen);
FileReader FileReader = new FileReader(@"C:\Download\CorpId-12345.mol");
//FileReader FileReader = new FileReader(@"C:\Download\V3000 Mols.sdf");
IteratingSDFReader rdr = new IteratingSDFReader(FileReader, DefaultChemObjectBuilder.getInstance());
rdr.setReaderMode(IChemObjectReader.Mode.RELAXED);
while (rdr.hasNext())
{
mol = (IAtomContainer)rdr.next();
mol = CdkMol.GetLargestMoleculeFragment(mol);
ICountFingerprint cfp1 = cfp.getCountFingerprint(mol); // get hash values and counts for each
cfp.calculate(mol);
int fpCount = cfp.getFPCount();
for (int fpi = 0; fpi < fpCount; fpi++) // gets
{
CircularFingerprinter.FP cfp2 = cfp.getFP(fpi); // gets hash, iteration and lists of atoms (dups appear multiple times)
}
IBitFingerprint bfp = cfp.getBitFingerprint(mol);
java.util.BitSet bs = bfp.asBitSet();
int bsCard = bfp.cardinality();
long bsSize = bfp.size();
continue;
}
FileReader.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();
}