public void TestFingerprint()
{
IFingerprinter printer = new PubchemFingerprinter();
var adder = CDK.HydrogenAdder;
var mol1 = parser.ParseSmiles("c1ccccc1CCc1ccccc1");
var mol2 = parser.ParseSmiles("c1ccccc1CC");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol2);
adder.AddImplicitHydrogens(mol1);
adder.AddImplicitHydrogens(mol2);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(mol1);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(mol2);
Aromaticity.CDKLegacy.Apply(mol1);
Aromaticity.CDKLegacy.Apply(mol2);
BitArray bs1 = printer.GetBitFingerprint(mol1).AsBitSet();
BitArray bs2 = printer.GetBitFingerprint(mol2).AsBitSet();
Assert.AreEqual(881, printer.Length);
Assert.IsFalse(FingerprinterTool.IsSubset(bs1, bs2),
"c1ccccc1CC was detected as a subset of c1ccccc1CCc1ccccc1");
}
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()));
}
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 TestDecode()
{
BitArray bitSet = PubchemFingerprinter
.Decode("AAADcYBgAAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGAAAAAAACACAEAAwAIAAAACAACBCAAACAAAgAAAIiAAAAIgIICKAERCAIAAggAAIiAcAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA==");
int[] setBits = new int[] { 0, 9, 10, 178, 179, 255, 283, 284, 332, 344, 355, 370, 371, 384, 416, 434, 441, 446,
470, 490, 516, 520, 524, 552, 556, 564, 570, 578, 582, 584, 595, 599, 603, 608, 618, 634, 640, 660,
664, 668, 677, 678, 679 };
foreach (var set in setBits)
{
Assert.IsTrue(bitSet[set], "bit " + set + " was not set");
}
}
public void Call()
{
BitArray fp = null;
IFingerprinter fpr = new PubchemFingerprinter();
try
{
fp = fpr.GetBitFingerprint(mol).AsBitSet();
}
catch (CDKException e)
{
Console.Error.WriteLine(e.StackTrace); //To change body of catch statement use File | Settings | File Templates.
}
Result = fp;
}
public void TestBenzene()
{
var mol = parser.ParseSmiles("c1ccccc1");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
var adder = CDK.HydrogenAdder;
adder.AddImplicitHydrogens(mol);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(mol);
Aromaticity.CDKLegacy.Apply(mol);
IFingerprinter printer = new PubchemFingerprinter();
BitArray fp = printer.GetBitFingerprint(mol).AsBitSet();
BitArray ref_ = PubchemFingerprinter
.Decode("AAADcYBgAAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGAAAAAAACACAEAAwAIAAAACAACBCAAACAAAgAAAIiAAAAIgIICKAERCAIAAggAAIiAcAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA==");
Assert.IsTrue(BitArrays.Equals(ref_, fp));
}
public void TestCID25181289()
{
var mol = parser.ParseSmiles("C=C(C1=CC=C(C=C1)O)NNC2=C(C(=NC(=C2Cl)Cl)C(=O)O)Cl");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
var adder = CDK.HydrogenAdder;
adder.AddImplicitHydrogens(mol);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(mol);
Aromaticity.CDKLegacy.Apply(mol);
IFingerprinter printer = new PubchemFingerprinter();
BitArray fp = printer.GetBitFingerprint(mol).AsBitSet();
BitArray ref_ = PubchemFingerprinter
.Decode("AAADccBzMAAGAAAAAAAAAAAAAAAAAAAAAAA8QAAAAAAAAAABwAAAHgIYCAAADA6BniAwzpJqEgCoAyTyTASChCAnJiIYumGmTtgKJnLD1/PEdQhkwBHY3Qe82AAOIAAAAAAAAABAAAAAAAAAAAAAAAAAAA==");
Assert.IsTrue(BitArrays.Equals(ref_, fp));
}
public void TestCID5934166()
{
var mol = parser.ParseSmiles("C1=CC=C(C=C1)C[N+]2=C(C=C(C=C2C=CC3=CC=CC=C3)C4=CC=CC=C4)C5=CC=CC=C5");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
var adder = CDK.HydrogenAdder;
adder.AddImplicitHydrogens(mol);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(mol);
Aromaticity.CDKLegacy.Apply(mol);
IFingerprinter printer = new PubchemFingerprinter();
BitArray fp = printer.GetBitFingerprint(mol).AsBitSet();
BitArray ref_ = PubchemFingerprinter
.Decode("AAADceB+AAAAAAAAAAAAAAAAAAAAAAAAAAA8YMGCAAAAAAAB1AAAHAAAAAAADAjBHgQwgJMMEACgAyRiRACCgCAhAiAI2CA4ZJgIIOLAkZGEIAhggADIyAcQgMAOgAAAAAAAAAAAAAAAAAAAAAAAAAAAAA==");
Assert.IsTrue(BitArrays.Equals(ref_, fp));
}
public void TestCID2518130()
{
var mol = parser.ParseSmiles("COC1C(C(C(C(O1)CO)OC2C(C(C(C(O2)CO)S)O)O)O)O");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
var adder = CDK.HydrogenAdder;
adder.AddImplicitHydrogens(mol);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(mol);
Aromaticity.CDKLegacy.Apply(mol);
IFingerprinter printer = new PubchemFingerprinter();
BitArray fp = printer.GetBitFingerprint(mol).AsBitSet();
BitArray ref_ = PubchemFingerprinter
.Decode("AAADceBwPABAAAAAAAAAAAAAAAAAAAAAAAAkSAAAAAAAAAAAAAAAGgQACAAACBS0wAOCCAAABgQAAAAAAAAAAAAAAAAAAAAAAAAREAIAAAAiQAAFAAAHAAHAYAwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA==");
Assert.IsTrue(BitArrays.Equals(ref_, fp));
}
public void TestMultithReadedUsage()
{
var mol1 = parser.ParseSmiles("C=C(C1=CC=C(C=C1)O)NNC2=C(C(=NC(=C2Cl)Cl)C(=O)O)Cl");
IAtomContainer mol2 = parser
.ParseSmiles("C1=CC=C(C=C1)C[N+]2=C(C=C(C=C2C=CC3=CC=CC=C3)C4=CC=CC=C4)C5=CC=CC=C5");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol2);
var adder = CDK.HydrogenAdder;
adder.AddImplicitHydrogens(mol1);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(mol1);
Aromaticity.CDKLegacy.Apply(mol1);
adder.AddImplicitHydrogens(mol2);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(mol2);
Aromaticity.CDKLegacy.Apply(mol2);
IFingerprinter fp = new PubchemFingerprinter();
BitArray bs1 = fp.GetBitFingerprint(mol1).AsBitSet();
BitArray bs2 = fp.GetBitFingerprint(mol2).AsBitSet();
// now lets run some threads
var objs = new List <FpRunner>
{
new FpRunner(mol1),
new FpRunner(mol2)
};
var ret = Parallel.ForEach(objs, o => o.Call());
Assert.IsTrue(ret.IsCompleted);
BitArray fb1 = objs[0].Result;
Assert.IsNotNull(fb1);
BitArray fb2 = objs[1].Result;
Assert.IsNotNull(fb2);
Assert.IsTrue(BitArrays.Equals(bs1, fb1));
Assert.IsTrue(BitArrays.Equals(bs2, fb2));
}
public void TestGetFingerprintAsBytes()
{
var mol = parser.ParseSmiles("C=C(C1=CC=C(C=C1)O)NNC2=C(C(=NC(=C2Cl)Cl)C(=O)O)Cl");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
var adder = CDK.HydrogenAdder;
adder.AddImplicitHydrogens(mol);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(mol);
Aromaticity.CDKLegacy.Apply(mol);
PubchemFingerprinter printer = new PubchemFingerprinter();
BitArray fp = printer.GetBitFingerprint(mol).AsBitSet();
byte[] actual = printer.GetFingerprintAsBytes();
byte[] expected = Arrays.CopyOf(ToByteArray(fp), actual.Length);
Assert.IsTrue(Compares.AreEqual(expected, actual));
}
public void Testfp2()
{
IFingerprinter printer = new PubchemFingerprinter();
var mol1 = parser.ParseSmiles("CC(N)CCCN");
var mol2 = parser.ParseSmiles("CC(N)CCC");
var mol3 = parser.ParseSmiles("CCCC");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol2);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol3);
Aromaticity.CDKLegacy.Apply(mol1);
Aromaticity.CDKLegacy.Apply(mol2);
Aromaticity.CDKLegacy.Apply(mol3);
BitArray bs1 = printer.GetBitFingerprint(mol1).AsBitSet();
BitArray bs2 = printer.GetBitFingerprint(mol2).AsBitSet();
BitArray bs3 = printer.GetBitFingerprint(mol3).AsBitSet();
Assert.IsTrue(FingerprinterTool.IsSubset(bs1, bs2));
Assert.IsTrue(FingerprinterTool.IsSubset(bs2, bs3));
}
public void TestGetSize()
{
IFingerprinter printer = new PubchemFingerprinter();
Assert.AreEqual(881, printer.Length);
}
public void TestDecode_invalid()
{
PubchemFingerprinter.Decode("a");
}
/// <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);
}
public void TestGetSize()
{
IFingerprinter printer = new PubchemFingerprinter(ChemObjectBuilder.Instance);
Assert.AreEqual(881, printer.Length);
}
