public void TestCyclopropaneNotASubgraphOfIsoButane()
{
IAtomContainer cycloPropane = CreateCyclopropane();
IAtomContainer isobutane = CreateIsobutane();
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(cycloPropane);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(isobutane);
IAtomContainer source = ExtAtomContainerManipulator.RemoveHydrogensExceptSingleAndPreserveAtomID(cycloPropane);
IAtomContainer target = ExtAtomContainerManipulator.RemoveHydrogensExceptSingleAndPreserveAtomID(isobutane);
Aromaticity.CDKLegacy.Apply(source);
Aromaticity.CDKLegacy.Apply(target);
bool bondSensitive = false;
bool removeHydrogen = true;
bool stereoMatch = true;
bool fragmentMinimization = true;
bool energyMinimization = true;
// Calling the main algorithm to perform MCS cearch
Isomorphism comparison = new Isomorphism(Algorithm.SubStructure, bondSensitive);
comparison.Init(source, target, removeHydrogen, true);
comparison.SetChemFilters(stereoMatch, fragmentMinimization, energyMinimization);
// Cyclopropane is not a subgraph of Isobutane
Assert.IsFalse(comparison.IsSubgraph());
Assert.AreEqual(0.625, comparison.GetTanimotoSimilarity());
}
public void TestSMSDFragHetSubgraph()
{
var sp = CDK.SmilesParser;
string file1 = "O=C1NC(=O)C2=C(N1)NC(=O)C=N2";
string file2 = "OC[C@@H](O)[C@@H](O)[C@@H](O)CN1C(O)C(CCC(O)O)NC2C(O)NC(O)NC12";
var mol1 = sp.ParseSmiles(file1);
var mol2 = sp.ParseSmiles(file2);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol1);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol2);
IAtomContainer source = ExtAtomContainerManipulator.RemoveHydrogensExceptSingleAndPreserveAtomID(mol1);
IAtomContainer target = ExtAtomContainerManipulator.RemoveHydrogensExceptSingleAndPreserveAtomID(mol2);
// Calling the main algorithm to perform MCS search
Aromaticity.CDKLegacy.Apply(source);
Aromaticity.CDKLegacy.Apply(target);
bool bondSensitive = false;
bool removeHydrogen = true;
bool stereoMatch = true;
bool fragmentMinimization = true;
bool energyMinimization = true;
Isomorphism comparison = new Isomorphism(Algorithm.Default, bondSensitive);
comparison.Init(source, target, removeHydrogen, true);
comparison.SetChemFilters(stereoMatch, fragmentMinimization, energyMinimization);
Assert.IsTrue(comparison.IsSubgraph());
Assert.AreEqual(13, comparison.GetFirstMapping().Count);
}
static VFLibTest()
{
hexane = CreateHexane();
Assert.AreEqual(6, hexane.Atoms.Count);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(hexane);
hexane = ExtAtomContainerManipulator.RemoveHydrogensExceptSingleAndPreserveAtomID(hexane);
Aromaticity.CDKLegacy.Apply(hexane);
hexaneQuery = new QueryCompiler(hexane, true).Compile();
Assert.AreEqual(6, hexaneQuery.CountNodes());
benzene = CreateBenzene();
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(benzene);
hexane = ExtAtomContainerManipulator.RemoveHydrogensExceptSingleAndPreserveAtomID(benzene);
Aromaticity.CDKLegacy.Apply(benzene);
benzeneQuery = new QueryCompiler(benzene, true).Compile();
}
public void TestSMSDLargeSubgraph()
{
var sp = CDK.SmilesParser;
string c03374 = "CC1=C(C=C)\\C(NC1=O)=C" + "\\C1=C(C)C(CCC(=O)O[C@@H]2O[C@@H]"
+ "([C@@H](O)[C@H](O)[C@H]2O)C(O)=O)" + "=C(CC2=C(CCC(O)=O)C(C)=C(N2)" + "\\C=C2NC(=O)C(C=C)=C/2C)N1";
string c05787 = "CC1=C(C=C)\\C(NC1=O)=C" + "\\C1=C(C)C(CCC(=O)O[C@@H]2O[C@@H]"
+ "([C@@H](O)[C@H](O)[C@H]2O)C(O)=O)" + "=C(CC2=C(CCC(=O)O[C@@H]3O[C@@H]"
+ "([C@@H](O)[C@H](O)[C@H]3O)C(O)=O)" + "C(C)=C(N2)" + "\\C=C2NC(=O)C(C=C)=C/2C)N1";
var mol1 = sp.ParseSmiles(c03374);
var mol2 = sp.ParseSmiles(c05787);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol1);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol2);
IAtomContainer source = ExtAtomContainerManipulator.RemoveHydrogensExceptSingleAndPreserveAtomID(mol1);
IAtomContainer target = ExtAtomContainerManipulator.RemoveHydrogensExceptSingleAndPreserveAtomID(mol2);
// Calling the main algorithm to perform MCS cearch
Aromaticity.CDKLegacy.Apply(source);
Aromaticity.CDKLegacy.Apply(target);
bool bondSensitive = true;
bool removeHydrogen = true;
bool stereoMatch = true;
bool fragmentMinimization = true;
bool energyMinimization = true;
Isomorphism comparison = new Isomorphism(Algorithm.SubStructure, bondSensitive);
comparison.Init(source, target, removeHydrogen, true);
comparison.SetChemFilters(stereoMatch, fragmentMinimization, energyMinimization);
Assert.IsTrue(comparison.IsSubgraph());
Assert.AreEqual(55, comparison.GetFirstMapping().Count);
}
/// <summary>
/// Returns IAtomContainer without Hydrogen. If an AtomContainer has atom single atom which
/// is atom Hydrogen then its not removed.
/// </summary>
/// <returns>IAtomContainer without Hydrogen. If an AtomContainer has atom single atom which is atom Hydrogen then its not removed.</returns>
public static IAtomContainer RemoveHydrogensAndPreserveAtomID(IAtomContainer atomContainer)
{
return(ExtAtomContainerManipulator.RemoveHydrogensExceptSingleAndPreserveAtomID(atomContainer));
}