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);
}
public void TestQueryAtomContainerSubstructure()
{
var sp = CDK.SmilesParser;
var query = sp.ParseSmiles("CC");
var target = sp.ParseSmiles("C1CCC12CCCC2");
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(query);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(target);
// Calling the main algorithm to perform MCS cearch
Aromaticity.CDKLegacy.Apply(query);
Aromaticity.CDKLegacy.Apply(target);
Isomorphism smsd = new Isomorphism(Algorithm.SubStructure, true);
smsd.Init(query, target, false, true);
bool foundMatches = smsd.IsSubgraph();
Assert.IsTrue(foundMatches);
// IQueryAtomContainer queryContainer = QueryAtomContainerCreator.CreateSymbolAndBondOrderQueryContainer(query);
//
// Isomorphism smsd1 = new Isomorphism(Algorithm.SubStructure, true);
// smsd1.Init(queryContainer, target, true, true);
// smsd1.SetChemFilters(true, true, true);
// foundMatches = smsd1.IsSubgraph();
// Assert.IsFalse(foundMatches);
}
public void TestGetAllAtomMapping()
{
var sp = new SmilesParser(ChemObjectBuilder.Instance, false);
var target = sp.ParseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
var queryac = sp.ParseSmiles("Nc1ccccc1");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(target);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(queryac);
Aromaticity.CDKLegacy.Apply(target);
Aromaticity.CDKLegacy.Apply(queryac);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(queryac);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(target);
// Calling the main algorithm to perform MCS cearch
Aromaticity.CDKLegacy.Apply(queryac);
Aromaticity.CDKLegacy.Apply(target);
Isomorphism smsd1 = new Isomorphism(Algorithm.Default, true);
smsd1.Init(queryac, target, true, true);
smsd1.SetChemFilters(true, true, true);
Assert.IsNotNull(smsd1.GetFirstMapping());
Assert.AreEqual(2, smsd1.GetAllAtomMapping().Count);
}
public void TestSMSDAdpAtpSubgraph()
{
var sp = CDK.SmilesParser;
string adp = "NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O";
string atp = "NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O";
var mol1 = sp.ParseSmiles(adp);
var mol2 = sp.ParseSmiles(atp);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol1);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol2);
// Calling the main algorithm to perform MCS cearch
Aromaticity.CDKLegacy.Apply(mol1);
Aromaticity.CDKLegacy.Apply(mol2);
bool bondSensitive = true;
bool removeHydrogen = true;
bool stereoMatch = true;
bool fragmentMinimization = true;
bool energyMinimization = true;
Isomorphism comparison = new Isomorphism(Algorithm.Default, bondSensitive);
comparison.Init(mol1, mol2, removeHydrogen, true);
comparison.SetChemFilters(stereoMatch, fragmentMinimization, energyMinimization);
// Get modified Query and Target Molecules as Mappings will correspond to these molecules
Assert.IsTrue(comparison.IsSubgraph());
Assert.AreEqual(2, comparison.GetAllMapping().Count);
Assert.AreEqual(27, comparison.GetFirstMapping().Count);
}
static SMSDBondInsensitiveTest()
{
Napthalene = CreateNaphthalene();
Cyclohexane = CreateCyclohexane();
Benzene = CreateBenzene();
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(Napthalene);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(Cyclohexane);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(Benzene);
Aromaticity.CDKLegacy.Apply(Napthalene);
Aromaticity.CDKLegacy.Apply(Cyclohexane);
Aromaticity.CDKLegacy.Apply(Benzene);
}
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);
}
public void TestSingleMappingTesting()
{
var sp = CDK.SmilesParser;
var atomContainer = sp.ParseSmiles("C");
IAtomContainer mol2 = Create4Toluene();
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol2);
Aromaticity.CDKLegacy.Apply(mol2);
bool bondSensitive = false;
bool removeHydrogen = true;
bool stereoMatch = false;
bool fragmentMinimization = false;
bool energyMinimization = false;
Isomorphism comparison = new Isomorphism(Algorithm.Default, bondSensitive);
comparison.Init(atomContainer, mol2, removeHydrogen, true);
comparison.SetChemFilters(stereoMatch, fragmentMinimization, energyMinimization);
Assert.IsTrue(comparison.IsSubgraph());
Assert.AreEqual(7, comparison.GetAllMapping().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));
}
/// <summary>
/// The summed implicit + explicit hydrogens of the given IAtom.
/// <returns>The summed implicit + explicit hydrogens of the given IAtom.</returns>
/// </summary>
public static int GetHydrogenCount(IAtomContainer atomContainer, IAtom atom)
{
return(ExtAtomContainerManipulator.GetHydrogenCount(atomContainer, atom));
}
/// <summary>
/// This function finds rings and uses aromaticity detection code to
/// aromatize the molecule.
/// </summary>
/// <param name="mol">input molecule</param>
public static void AromatizeMolecule(IAtomContainer mol)
{
ExtAtomContainerManipulator.AromatizeMolecule(mol);
}
/// <summary>
/// Convenience method to perceive atom types for all <see cref="IAtom"/>s in the
/// <see cref="IAtomContainer"/>, using the <see cref="AtomTypes.CDKAtomTypeMatcher"/>. If the
/// matcher finds atom matching atom type, the <see cref="IAtom"/> will be configured
/// to have the same properties as the <see cref="IAtomType"/>. If no matching atom
/// type is found, no configuration is performed.
/// <param name="container"></param>
/// </summary>
/// <exception cref="CDKException"></exception>
public static void PercieveAtomTypesAndConfigureAtoms(IAtomContainer container)
{
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(container);
}
/// <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 ConvertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
{
return(ExtAtomContainerManipulator.ConvertExplicitToImplicitHydrogens(atomContainer));
}
