public void TestAnonFingerprints()
{
var expected = new BitArray[]
{
ParseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
ParseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
ParseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
ParseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
ParseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
ParseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
ParseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
ParseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
ParseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
ParseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
};
var filename = "NCDK.Data.MDL.fingerprints_from_modelbuilder3d.sdf";
var ins = this.GetType().Assembly.GetManifestResourceStream(filename);
var data = TemplateExtractor.MakeFingerprintsFromSdf(true, true,
new Dictionary <string, int>(), new StreamReader(ins), 10);
var obj = new QueryChemObject();
var dummy = obj.Builder;
for (int i = 0; i < data.Count; i++)
{
IBitFingerprint bs = data[i];
Assert.IsTrue(Compares.AreEqual(expected[i], bs.AsBitSet()));
}
}
public override void TestBug706786()
{
IAtomContainer superStructure = Bug706786_1();
IAtomContainer subStructure = Bug706786_2();
AddImplicitHydrogens(superStructure);
AddImplicitHydrogens(subStructure);
// SMARTS is now correct and D will include H atoms, CDK had this wrong
// for years (had it has non-H count). Whilst you can set the optional
// SMARTS flavor CDK_LEGACY this is not correct
AtomContainerManipulator.SuppressHydrogens(superStructure);
AtomContainerManipulator.SuppressHydrogens(subStructure);
IFingerprinter fpr = GetBitFingerprinter();
IBitFingerprint superBits = fpr.GetBitFingerprint(superStructure);
IBitFingerprint subBits = fpr.GetBitFingerprint(subStructure);
Assert.IsTrue(BitArrays.Equals(
AsBitSet(0, 11, 13, 17, 40, 48, 136, 273, 274, 278, 286, 294, 299, 301, 304, 306),
superBits.AsBitSet()));
Assert.IsTrue(BitArrays.Equals(
AsBitSet(1, 17, 273, 274, 278, 294, 306),
subBits.AsBitSet()));
}
public override void TestBug934819()
{
IAtomContainer subStructure = Bug934819_1();
IAtomContainer superStructure = Bug934819_2();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(superStructure);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(subStructure);
AddImplicitHydrogens(superStructure);
AddImplicitHydrogens(subStructure);
IFingerprinter fpr = new PubchemFingerprinter();
IBitFingerprint superBits = fpr.GetBitFingerprint(superStructure);
IBitFingerprint subBits = fpr.GetBitFingerprint(subStructure);
Assert.IsTrue(BitArrays.Equals(
AsBitSet(9, 10, 14, 18, 19, 33, 143, 146, 255, 256, 283, 284, 285, 293, 301, 332, 344, 349, 351,
353, 355, 368, 370, 371, 376, 383, 384, 395, 401, 412, 416, 421, 423, 434, 441, 446, 449, 454,
455, 464, 470, 471, 480, 489, 490, 500, 502, 507, 513, 514, 516, 520, 524, 531, 532, 545, 546,
549, 552, 556, 558, 564, 570, 586, 592, 599, 600, 607, 633, 658, 665),
subBits.AsBitSet()));
Assert.IsTrue(BitArrays.Equals(
AsBitSet(9, 10, 11, 14, 18, 19, 33, 34, 143, 146, 150, 153, 255, 256, 257, 258, 283, 284, 285, 293,
301, 332, 344, 349, 351, 353, 355, 368, 370, 371, 374, 376, 383, 384, 395, 401, 412, 416, 417,
421, 423, 427, 434, 441, 446, 449, 454, 455, 460, 464, 470, 471, 479, 480, 489, 490, 500, 502,
507, 513, 514, 516, 520, 524, 531, 532, 545, 546, 549, 552, 556, 558, 564, 570, 578, 582, 584,
586, 592, 595, 600, 603, 607, 608, 633, 634, 640, 658, 660, 664, 665, 668, 677, 678, 683),
superBits.AsBitSet()));
}
private IBitFingerprint CreateFP2()
{
IBitFingerprint fp = (IBitFingerprint)C.GetConstructor(Type.EmptyTypes).Invoke(new object[] { });
fp[2] = true;
fp[3] = true;
return(fp);
}
/// <summary>
/// While this test fails, Daylight says that the
/// SMARTS pattern used for vinylogous ester should
/// match benzaldehyde twice. So according to the
/// supplied definition this answer is actually correct.
/// </summary>
// @cdk.bug 2871303
//("the SMARTS pattern vinylogous ester is not strict enough - we can not fix this")
public static void TestVinylogousEster()
{
string benzaldehyde = "c1ccccc1C=O";
IFingerprinter fprinter = new SubstructureFingerprinter();
var sp = CDK.SmilesParser;
IBitFingerprint fp = fprinter.GetBitFingerprint(sp.ParseSmiles(benzaldehyde));
Assert.IsFalse(fp[136], "Bit 136 (vinylogous ester) is set to true");
}
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 TestFingerprint()
{
var parser = CDK.SmilesParser;
IFingerprinter printer = new GraphOnlyFingerprinter();
IBitFingerprint bs1 = printer.GetBitFingerprint(parser.ParseSmiles("C=C-C#N"));
IBitFingerprint bs2 = printer.GetBitFingerprint(parser.ParseSmiles("CCCN"));
Assert.AreEqual(bs1, bs2);
}
public static string ToExcelString(IBitFingerprint fp)
{
var sb = new StringBuilder();
for (int i = 0; i < fp.Length; i++)
{
sb.Append(fp[i] ? "1" : "0");
}
return(sb.ToString());
}
public static void Main()
{
{
#region
var molecule = new AtomContainer();
IFingerprinter fingerprinter = new PubchemFingerprinter(Silent.ChemObjectBuilder.Instance);
IBitFingerprint fingerprint = fingerprinter.GetBitFingerprint(molecule);
Console.WriteLine(fingerprint.Length); // returns 881
#endregion
}
}
public void Or(IBitFingerprint fingerprint)
{
if (fingerprint is IntArrayFingerprint)
{
Or((IntArrayFingerprint)fingerprint);
}
else
{
//TODO add support for this?
throw new NotSupportedException("OR on IntArrayFingerPrint only supported for other IntArrayFingerPrints for the moment");
}
}
public void TestgetBitFingerprint_IAtomContainer()
{
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter();
IAtomContainer mol = TestMoleculeFactory.MakeIndole();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
IBitFingerprint bs = fingerprinter.GetBitFingerprint(mol);
Assert.IsNotNull(bs);
Assert.AreEqual(fingerprinter.Length, bs.Length);
}
public void TestFingerprint()
{
var parser = CDK.SmilesParser;
IFingerprinter printer = new EStateFingerprinter();
IBitFingerprint bs1 = printer.GetBitFingerprint(parser.ParseSmiles("C=C-C#N"));
IBitFingerprint bs2 = printer.GetBitFingerprint(parser.ParseSmiles("C=CCC(O)CC#N"));
Assert.AreEqual(79, printer.Length);
Assert.IsTrue(bs1[7]);
Assert.IsTrue(bs1[10]);
Assert.IsTrue(FingerprinterTool.IsSubset(bs2.AsBitSet(), bs1.AsBitSet()));
}
public void TestAtomPermutation()
{
IAtomContainer pamine = MakePropylAmine();
ShortestPathFingerprinter fp = new ShortestPathFingerprinter();
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 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 TestEquals()
{
IBitFingerprint fp1 = (IBitFingerprint)C.GetConstructor(Type.EmptyTypes).Invoke(new object[] { });
IBitFingerprint fp2 = (IBitFingerprint)C.GetConstructor(Type.EmptyTypes).Invoke(new object[] { });
foreach (var fp in new IBitFingerprint[] { fp1, fp2 })
{
fp[0] = true;
fp[1] = false;
fp[2] = true;
}
Assert.IsTrue(fp1.Equals(fp2), "identical fingerprints should be equal");
Assert.IsFalse(bitsetFP.Equals(fp1), "different fingerprints should not be equal");
Assert.IsTrue(fp1.GetHashCode() == fp2.GetHashCode(), "equal fingerprints must have same hashcode");
}
public void TestRegression()
{
IAtomContainer mol1 = TestMoleculeFactory.MakeIndole();
IAtomContainer mol2 = TestMoleculeFactory.MakePyrrole();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol2);
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter();
IBitFingerprint bs1 = fingerprinter.GetBitFingerprint(mol1);
Assert.AreEqual(22, 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(11, bs2.Cardinality, "Seems the fingerprint code has changed. This will cause a number of other tests to fail too!");
}
public void TestFunctionalGroupsBinary()
{
var printer = new SubstructureFingerprinter();
Assert.AreEqual(307, printer.Length);
var sp = CDK.SmilesParser;
var mol1 = sp.ParseSmiles("c1ccccc1CCC");
IBitFingerprint fp = printer.GetBitFingerprint(mol1);
Assert.IsNotNull(fp);
Assert.IsTrue(fp[273]);
Assert.IsTrue(fp[0]);
Assert.IsTrue(fp[1]);
Assert.IsFalse(fp[100]);
}
public BitSetFingerprint(IBitFingerprint fingerprint)
{
if (fingerprint is BitSetFingerprint)
{
bitset = (BitArray)((BitSetFingerprint)fingerprint).bitset.Clone();
}
else
{
var bitSet = new BitArray((int)fingerprint.Length);
for (int i = 0; i < fingerprint.Length; i++)
{
bitSet.Set(i, fingerprint[i]);
}
this.bitset = bitSet;
}
}
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 TestAtomPermutation2()
{
IAtomContainer pamine = TestMoleculeFactory.MakeCyclopentane();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(pamine);
ShortestPathFingerprinter fp = new ShortestPathFingerprinter();
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 Or(IBitFingerprint fingerprint)
{
if (bitset.Count != fingerprint.Length)
{
throw new ArgumentException("Fingerprints must have same size");
}
if (fingerprint is BitSetFingerprint)
{
bitset.Or(((BitSetFingerprint)fingerprint).bitset);
}
else
{
for (int i = 0; i < bitset.Count; i++)
{
bitset.Set(i, bitset[i] || fingerprint[i]);
}
}
}
/// <summary>
/// Evaluates Tanimoto coefficient for two <see cref="IBitFingerprint"/>.
/// </summary>
/// <param name="fingerprint1">fingerprint for the first molecule</param>
/// <param name="fingerprint2">fingerprint for the second molecule</param>
/// <returns>The Tanimoto coefficient</returns>
/// <exception cref="ArgumentException">if bitsets are not of the same length</exception>
public static double Calculate(IBitFingerprint fingerprint1, IBitFingerprint fingerprint2)
{
if (fingerprint1.Length != fingerprint2.Length)
{
throw new ArgumentException("Fingerprints must have the same size");
}
int cardinality1 = fingerprint1.Cardinality;
int cardinality2 = fingerprint2.Cardinality;
// If the fingerprint is an IntArrayFingeprint that could mean a big
// fingerprint so let's take the safe way out and create a
// new IntArrayfingerprint
IBitFingerprint one_and_two = fingerprint1 is IntArrayFingerprint ? (IBitFingerprint) new IntArrayFingerprint(
fingerprint1) : (IBitFingerprint) new BitSetFingerprint(fingerprint1);
one_and_two.And(fingerprint2);
double cardinalityCommon = one_and_two.Cardinality;
return(cardinalityCommon / (cardinality1 + cardinality2 - cardinalityCommon));
}
public IntArrayFingerprint(IBitFingerprint fingerprint)
{
// if it is an IntArrayFingerprint we can do faster (Array.Copy)
if (fingerprint is IntArrayFingerprint iaFP)
{
trueBits = new int[iaFP.trueBits.Length];
Array.Copy(iaFP.trueBits, 0, trueBits, 0, trueBits.Length);
}
else
{
trueBits = new int[fingerprint.Cardinality];
int index = 0;
for (int i = 0; i < fingerprint.Length; i++)
{
if (fingerprint[i])
{
trueBits[index++] = i;
}
}
}
}
public override void TestBug706786()
{
IAtomContainer superStructure = Bug706786_1();
IAtomContainer subStructure = Bug706786_2();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(superStructure);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(subStructure);
AddImplicitHydrogens(superStructure);
AddImplicitHydrogens(subStructure);
IFingerprinter fpr = new MACCSFingerprinter();
IBitFingerprint superBits = fpr.GetBitFingerprint(superStructure);
IBitFingerprint subBits = fpr.GetBitFingerprint(subStructure);
Assert.IsTrue(BitArrays.Equals(
AsBitSet(53, 56, 65, 71, 73, 88, 97, 104, 111, 112, 126, 130, 136, 138, 139, 140, 142, 143,
144, 145, 148, 149, 151, 153, 156, 158, 159, 161, 162, 163, 164),
superBits.AsBitSet()));
Assert.IsTrue(BitArrays.Equals(
AsBitSet(56, 97, 104, 108, 112, 117, 131, 136, 143, 144, 146, 151, 152, 156, 161, 162, 163, 164),
subBits.AsBitSet()));
}
public override void TestBug706786()
{
IAtomContainer superStructure = Bug706786_1();
IAtomContainer subStructure = Bug706786_2();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(superStructure);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(subStructure);
AddImplicitHydrogens(superStructure);
AddImplicitHydrogens(subStructure);
// SMARTS is now correct and D will include H atoms, CDK had this wrong
// for years (had it has non-H count). Whilst you can set the optional
// SMARTS flavor CDK_LEGACY this is not correct
AtomContainerManipulator.SuppressHydrogens(superStructure);
AtomContainerManipulator.SuppressHydrogens(subStructure);
IFingerprinter fpr = new EStateFingerprinter();
IBitFingerprint superBits = fpr.GetBitFingerprint(superStructure);
IBitFingerprint subBits = fpr.GetBitFingerprint(subStructure);
Assert.IsTrue(BitArrays.Equals(AsBitSet(6, 11, 12, 15, 16, 18, 33, 34, 35), superBits.AsBitSet()));
Assert.IsTrue(BitArrays.Equals(AsBitSet(8, 11, 16, 35), subBits.AsBitSet()));
}
public void TestUserFunctionalGroups()
{
string[] smarts = { "c1ccccc1", "[CX4H3][#6]", "[CX2]#[CX2]" };
var printer = new SubstructureFingerprinter(smarts);
Assert.AreEqual(3, printer.Length);
var sp = CDK.SmilesParser;
var mol1 = sp.ParseSmiles("c1ccccc1CCC");
IBitFingerprint fp = printer.GetBitFingerprint(mol1);
Assert.IsNotNull(fp);
Assert.IsTrue(fp[0]);
Assert.IsTrue(fp[1]);
Assert.IsFalse(fp[2]);
mol1 = sp.ParseSmiles("C=C=C");
fp = printer.GetBitFingerprint(mol1);
Assert.IsNotNull(fp);
Assert.IsFalse(fp[0]);
Assert.IsFalse(fp[1]);
Assert.IsFalse(fp[2]);
}
private Type C; // : IBitFingerprint
public AbstractBitFingerprintTest(Type C)
{
this.C = C;
bitsetFP = (IBitFingerprint)C.GetConstructor(Type.EmptyTypes).Invoke(new object[] { });
}
/// <summary>
/// Build fingerprint
/// </summary>
/// <param name="mol"></param>
public static BitSetFingerprint BuildBitSetFingerprint(
IAtomContainer mol,
FingerprintType fpType,
int fpSubtype = -1,
int fpLen = -1)
{
// Data for Tanimoto similarity using various fingerprint types for CorpId 123456 query.
// Cart - Standard MDL Oracle Cartridge scores
//
// Similarity Score
// ------------------------------------------------
// Size -> 192 896 1024 1024 128 1024 320
// CorpId Cart MACCS PbChm ECFP4 EXT EState Basic Sbstr
// ------ ---- ---- ---- ---- ---- ---- ---- ----
// 123456 0.99 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.99 0.98 0.96 0.77 0.95 1.00 0.95 1.00
// 123456 0.99 0.98 0.96 0.77 0.95 1.00 0.94 1.00
// 123456 0.99 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.99 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.99 0.91 1.00 0.81 1.00 1.00 1.00 1.00
// 123456 0.98 0.95 1.00 0.74 0.92 1.00 0.93 0.94
// 123456 0.98 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.98 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.98 1.00 0.83 0.76 0.77 0.90 0.76 0.94
// LSH Bin Count - The number of LSH bins (of 25) that match the query bin values
//--------------
// CorpId MAC PbC ECFP EX
// ------ --- --- --- ---
// 123456 25 25 25 25
// 123456 25 20 7 16
// 123456 25 20 9 19
// 123456 25 25 25 25
// 123456 25 25 25 25
// 123456 20 25 9 25
// 123456 21 25 11 17
// 123456 25 25 25 25
// 123456 25 25 25 25
// 123456 25 9 6 11
// Data for Tanimoto similarity using various Circular fingerprint types.
// Using 2 molecules where the 2nd just has an added methyl group.
//
// Measure Score
// -------- -----
// ECFP0 1.00
// ECFP2 .88
// ECFP4 .75
// ECFP6 .64
// FCFP0 1.00
// FCFP2 .92
// FCFP4 .84
// FCFP6 .74
IFingerprinter ifptr = null;
IBitFingerprint ibfp = null;
BitSetFingerprint bfp = null;
IAtomContainer mol2;
string s = "";
DateTime t0 = DateTime.Now;
double getFptrTime = 0, buildFpTime = 0;
if (fpType == FingerprintType.Basic) // size = 1024
{
ifptr = new Fingerprinter();
}
else if (fpType == FingerprintType.Circular) // size variable
{
CircularFingerprinterClass cfpClass = (CircularFingerprinterClass)fpSubtype;
if (cfpClass < CircularFingerprinterClass.ECFP0 || cfpClass > CircularFingerprinterClass.ECFP6)
{
cfpClass = (CircularFingerprinterClass)CircularFingerprintType.DefaultCircularClass; // default class
}
if (fpLen < 0)
{
fpLen = CircularFingerprintType.DefaultCircularLength; // default length
}
ifptr = new CircularFingerprinter(cfpClass, fpLen);
//CircularFingerprinter cfp = (CircularFingerprinter)ifptr;
//ICountFingerprint cntFp = cfp.getCountFingerprint(mol); // debug
//s = CircularFpToString(cfp); // debug
}
else if (fpType == FingerprintType.Extended) // size = 1024
{
ifptr = new ExtendedFingerprinter(); // use DEFAULT_SIZE and DEFAULT_SEARCH_DEPTH
}
else if (fpType == FingerprintType.EState) // size = 128
{
ifptr = new EStateFingerprinter(); // use DEFAULT_SIZE and DEFAULT_SEARCH_DEPTH
}
else if (fpType == FingerprintType.MACCS) // size = 192
{
if (MACCSFp == null)
{
MACCSFp = new MACCSFingerprinter();
}
ifptr = MACCSFp;
}
else if (fpType == FingerprintType.PubChem) // size = 896
{
//IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
ifptr = new PubchemFingerprinter();
}
else if (fpType == FingerprintType.ShortestPath) // size =
{
ifptr = new ShortestPathFingerprinter(); // fails with atom type issue for many structures (e.g. 123456)
}
else if (fpType == FingerprintType.Signature) // size =
{
ifptr = new SignatureFingerprinter(); // can't convert array fingerprint to bitsetfingerprint
}
else if (fpType == FingerprintType.Substructure) // size = 320
{
ifptr = new SubstructureFingerprinter();
}
else
{
throw new Exception("Invalid CdkFingerprintType: " + fpType);
}
getFptrTime = TimeOfDay.Delta(ref t0);
ibfp = ifptr.GetBitFingerprint(mol);
bfp = (BitSetFingerprint)ibfp;
buildFpTime = TimeOfDay.Delta(ref t0);
//long size = bfp.size();
//int card = bfp.Cardinality;
return(bfp);
}
/// <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();
}
