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(); }