public void TestSFBug999330()
{
var file1 = "NCDK.Data.MDL.5SD.mol";
var file2 = "NCDK.Data.MDL.ADN.mol";
var mol1 = builder.NewAtomContainer();
using (var reader = new MDLV2000Reader(ResourceLoader.GetAsStream(file1), ChemObjectReaderMode.Strict))
{
reader.Read(mol1);
}
var mol2 = builder.NewAtomContainer();
using (var reader = new MDLV2000Reader(ResourceLoader.GetAsStream(file2), ChemObjectReaderMode.Strict))
{
reader.Read(mol2);
}
var permutor = new AtomContainerAtomPermutor(mol2);
permutor.MoveNext();
mol2 = builder.NewAtomContainer(permutor.Current);
var list1 = uiTester.GetOverlaps(mol1, mol2);
var list2 = uiTester.GetOverlaps(mol2, mol1);
Assert.AreEqual(1, list1.Count);
Assert.AreEqual(1, list2.Count);
Assert.AreEqual(list1[0].Atoms.Count, list2[0].Atoms.Count);
}
public void FullPermutationTest(IAtomContainer mol)
{
AtomContainerAtomPermutor permutor = new AtomContainerAtomPermutor(mol);
string expected = new MoleculeSignature(mol).ToCanonicalString();
int numberOfPermutationsTried = 0;
while (permutor.HasNext())
{
permutor.MoveNext();
IAtomContainer permutation = permutor.Current;
string actual = new MoleculeSignature(permutation).ToCanonicalString();
numberOfPermutationsTried++;
Assert.AreEqual(expected, actual, $"Failed on permutation{numberOfPermutationsTried}");
}
}
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 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));
}
}
/// <summary>
/// This test is checking all permutations of an atom container to see
/// if the refiner gives the canonical labelling map (effectively).
/// </summary>
/// <param name="atomContainer"></param>
public void CheckForCanonicalForm(IAtomContainer atomContainer)
{
AtomContainerAtomPermutor permutor = new AtomContainerAtomPermutor(atomContainer);
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
refiner.Refine(atomContainer);
Permutation best = refiner.GetBest().Invert();
string cert = AtomContainerPrinter.ToString(atomContainer, best, true);
while (permutor.MoveNext())
{
IAtomContainer permutedContainer = permutor.Current;
refiner.Refine(permutedContainer);
best = refiner.GetBest().Invert();
string permCert = AtomContainerPrinter.ToString(permutedContainer, best, true);
Assert.AreEqual(cert, permCert);
}
}
public void TestSFBug999330()
{
var file1 = "NCDK.Data.MDL.5SD.mol";
var file2 = "NCDK.Data.MDL.ADN.mol";
var mol1 = builder.NewAtomContainer();
var mol2 = builder.NewAtomContainer();
var ins1 = ResourceLoader.GetAsStream(file1);
new MDLV2000Reader(ins1, ChemObjectReaderMode.Strict).Read(mol1);
var ins2 = ResourceLoader.GetAsStream(file2);
new MDLV2000Reader(ins2, ChemObjectReaderMode.Strict).Read(mol2);
var permutor = new AtomContainerAtomPermutor(mol2);
permutor.MoveNext();
mol2 = builder.NewAtomContainer(permutor.Current);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol1);
var adder = CDK.HydrogenAdder;
adder.AddImplicitHydrogens(mol1);
Aromaticity.CDKLegacy.Apply(mol1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol2);
adder = CDK.HydrogenAdder;
adder.AddImplicitHydrogens(mol2);
Aromaticity.CDKLegacy.Apply(mol2);
var list1 = CDKMCS.GetOverlaps(mol1, mol2, true);
var list2 = CDKMCS.GetOverlaps(mol2, mol1, true);
Assert.AreEqual(1, list1.Count);
Assert.AreEqual(1, list2.Count);
Assert.AreEqual(list1[0].Atoms.Count, list2[0].Atoms.Count);
}