public void TestBug853254()
{
var builder = CDK.Builder;
var filename = "NCDK.Data.MDL.bug853254-2.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins, ChemObjectReaderMode.Strict);
IAtomContainer superstructure = (IAtomContainer)reader.Read(builder.NewAtomContainer());
filename = "NCDK.Data.MDL.bug853254-1.mol";
ins = ResourceLoader.GetAsStream(filename);
reader = new MDLV2000Reader(ins, ChemObjectReaderMode.Strict);
IAtomContainer substructure = (IAtomContainer)reader.Read(builder.NewAtomContainer());
// these molecules are different resonance forms of the same molecule
// make sure aromaticity is detected. although some fingerprinters do this
// one should not expected all implementations to do so.
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(superstructure);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(substructure);
Aromaticity.CDKLegacy.Apply(superstructure);
Aromaticity.CDKLegacy.Apply(substructure);
IFingerprinter fingerprinter = GetBitFingerprinter();
BitArray superBS = fingerprinter.GetBitFingerprint(superstructure).AsBitSet();
BitArray subBS = fingerprinter.GetBitFingerprint(substructure).AsBitSet();
bool isSubset = FingerprinterTool.IsSubset(superBS, subBS);
Assert.IsTrue(isSubset);
}
public void TestBug931608()
{
var builder = CDK.Builder;
var filename = "NCDK.Data.MDL.bug931608-1.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins, ChemObjectReaderMode.Strict);
IAtomContainer structure1 = (IAtomContainer)reader.Read(builder.NewAtomContainer());
filename = "NCDK.Data.MDL.bug931608-2.mol";
ins = ResourceLoader.GetAsStream(filename);
reader = new MDLV2000Reader(ins, ChemObjectReaderMode.Strict);
IAtomContainer structure2 = (IAtomContainer)reader.Read(builder.NewAtomContainer());
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(structure1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(structure2);
IFingerprinter fingerprinter = GetBitFingerprinter();
BitArray bs1 = fingerprinter.GetBitFingerprint(structure1).AsBitSet();
BitArray bs2 = fingerprinter.GetBitFingerprint(structure2).AsBitSet();
// now we do the bool XOR on the two bitsets, leading
// to a bitset that has all the bits set to "true" which differ
// between the two original bitsets
bs1.Xor(bs2);
// cardinality gives us the number of "true" bits in the
// result of the XOR operation.
int cardinality = BitArrays.Cardinality(bs1);
Assert.AreEqual(0, cardinality);
}
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 virtual void TestBug934819()
{
// inlined molecules - note this test fails if implicit hydrogens are
// included. generally PubCheMFingerprint can't be used for substructure filter
IAtomContainer superStructure = Bug934819_2();
IAtomContainer subStructure = Bug934819_1();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(superStructure);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(subStructure);
AddImplicitHydrogens(superStructure);
AddImplicitHydrogens(subStructure);
IFingerprinter fingerprinter = GetBitFingerprinter();
BitArray superBS = fingerprinter.GetBitFingerprint(superStructure).AsBitSet();
BitArray subBS = fingerprinter.GetBitFingerprint(subStructure).AsBitSet();
Assert.IsTrue(BitArrays.Equals(subBS, And(superBS, subBS)));
}
public virtual void TestBug706786()
{
// inlined molecules - note this test fails if implicit hydrogens are
// included. generally MACCS and ESTATE can't be used for substructure filter
// check those subclasses which check the bits are set
IAtomContainer superStructure = Bug706786_1();
IAtomContainer subStructure = Bug706786_2();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(superStructure);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(subStructure);
AddImplicitHydrogens(superStructure);
AddImplicitHydrogens(subStructure);
IFingerprinter fingerprinter = GetBitFingerprinter();
BitArray superBS = fingerprinter.GetBitFingerprint(superStructure).AsBitSet();
BitArray subBS = fingerprinter.GetBitFingerprint(subStructure).AsBitSet();
Assert.IsTrue(BitArrays.Equals(subBS, And(superBS, subBS)));
}
public void TestBug771485()
{
var builder = CDK.Builder;
var filename = "NCDK.Data.MDL.bug771485-1.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins, ChemObjectReaderMode.Strict);
IAtomContainer structure1 = (IAtomContainer)reader.Read(builder.NewAtomContainer());
filename = "NCDK.Data.MDL.bug771485-2.mol";
ins = ResourceLoader.GetAsStream(filename);
reader = new MDLV2000Reader(ins, ChemObjectReaderMode.Strict);
IAtomContainer structure2 = (IAtomContainer)reader.Read(builder.NewAtomContainer());
// these molecules are different resonance forms of the same molecule
// make sure aromaticity is detected. although some fingerprinters do this
// one should not expected all implementations to do so.
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(structure1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(structure2);
Aromaticity.CDKLegacy.Apply(structure1);
Aromaticity.CDKLegacy.Apply(structure2);
AddImplicitHydrogens(structure1);
AddImplicitHydrogens(structure2);
Kekulization.Kekulize(structure1);
Kekulization.Kekulize(structure2);
// hydrogens loaded from MDL mol files if non-query. Structure 2 has
// query aromatic bonds and the hydrogen counts are not assigned - ensure
// this is done here.
CDK.HydrogenAdder.AddImplicitHydrogens(structure1);
CDK.HydrogenAdder.AddImplicitHydrogens(structure2);
IFingerprinter fingerprinter = GetBitFingerprinter();
BitArray superBS = fingerprinter.GetBitFingerprint(structure2).AsBitSet();
BitArray subBS = fingerprinter.GetBitFingerprint(structure1).AsBitSet();
bool isSubset = FingerprinterTool.IsSubset(superBS, subBS);
Assert.IsTrue(isSubset);
}