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);
}
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 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 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 TestSMSD()
{
// Isomorphism ebimcs = new Isomorphism(Algorithm.VFLibMCS, true);
// ebimcs.Init(Cyclohexane, Benzene, true, true);
// ebimcs.SetChemFilters(true, true, true);
// Assert.AreEqual(1, ebimcs.GetFirstMapping().Count);
Isomorphism ebimcs1 = new Isomorphism(Algorithm.Default, true);
ebimcs1.Init(Benzene, Napthalene, true, true);
ebimcs1.SetChemFilters(true, true, true);
Assert.AreEqual(6, ebimcs1.GetFirstAtomMapping().Count);
ebimcs1 = new Isomorphism(Algorithm.Default, false);
ebimcs1.Init(Benzene, Napthalene, true, true);
ebimcs1.SetChemFilters(true, true, true);
Assert.AreEqual(6, ebimcs1.GetFirstAtomMapping().Count);
ebimcs1 = new Isomorphism(Algorithm.VFLibMCS, true);
ebimcs1.Init(Benzene, Napthalene, true, true);
ebimcs1.SetChemFilters(true, true, true);
Assert.AreEqual(6, ebimcs1.GetFirstAtomMapping().Count);
ebimcs1 = new Isomorphism(Algorithm.CDKMCS, true);
ebimcs1.Init(Benzene, Napthalene, true, true);
ebimcs1.SetChemFilters(true, true, true);
Assert.AreEqual(6, ebimcs1.GetFirstAtomMapping().Count);
ebimcs1 = new Isomorphism(Algorithm.MCSPlus, true);
ebimcs1.Init(Benzene, Napthalene, true, true);
ebimcs1.SetChemFilters(true, true, true);
Assert.AreEqual(6, ebimcs1.GetFirstAtomMapping().Count);
}
public void TestSMSD()
{
Isomorphism ebimcs = new Isomorphism(Algorithm.Default, false);
ebimcs.Init(Cyclohexane, Benzene, true, true);
ebimcs.SetChemFilters(true, true, true);
Assert.AreEqual(6, ebimcs.GetFirstMapping().Count);
}
public void TestSubgraph()
{
Isomorphism sbf = new Isomorphism(Algorithm.SubStructure, false);
sbf.Init(Benzene, Benzene, true, true);
sbf.SetChemFilters(false, false, false);
Assert.IsTrue(sbf.IsSubgraph());
}
public void TestVFLib()
{
Isomorphism sbf = new Isomorphism(Algorithm.VFLibMCS, true);
sbf.Init(Benzene, Benzene, true, true);
sbf.SetChemFilters(true, true, true);
Assert.IsTrue(sbf.IsSubgraph());
}
public void TestSMSDCyclohexaneBenzeneSubgraph()
{
Isomorphism ebimcs1 = new Isomorphism(Algorithm.SubStructure, false);
ebimcs1.Init(Cyclohexane, Benzene, true, true);
ebimcs1.SetChemFilters(true, true, true);
Assert.IsTrue(ebimcs1.IsSubgraph());
}
public void TestSMSDChemicalFilters()
{
Isomorphism ebimcs = new Isomorphism(Algorithm.Default, false);
ebimcs.Init(Cyclohexane, Benzene, true, true);
ebimcs.SetChemFilters(true, true, true);
Assert.AreEqual(12, ebimcs.GetAllMapping().Count);
Assert.IsTrue(ebimcs.IsSubgraph());
}
public void TestSMSDChemicalFilters()
{
Isomorphism ebimcs1 = new Isomorphism(Algorithm.Default, true);
ebimcs1.Init(Napthalene, Benzene, true, true);
ebimcs1.SetChemFilters(true, true, true);
Assert.AreEqual(6, ebimcs1.GetAllMapping().Count);
Assert.IsFalse(ebimcs1.IsSubgraph());
}
public void TestCDKMCS()
{
Isomorphism ebimcs = new Isomorphism(Algorithm.CDKMCS, false);
ebimcs.Init(Cyclohexane, Benzene, true, true);
ebimcs.SetChemFilters(true, true, true);
Assert.AreEqual(6, ebimcs.GetFirstMapping().Count);
Assert.IsTrue(ebimcs.IsSubgraph());
}
public void TestMCSPlus()
{
//TO DO fix me this error
Isomorphism ebimcs = new Isomorphism(Algorithm.MCSPlus, false);
ebimcs.Init(Cyclohexane, Benzene, true, true);
ebimcs.SetChemFilters(true, true, true);
Assert.IsTrue(ebimcs.IsSubgraph());
}
public void TestSubgraph()
{
Isomorphism sbf = new Isomorphism(Algorithm.SubStructure, true);
sbf.Init(Benzene, Napthalene, true, true);
sbf.SetChemFilters(false, false, false);
Assert.IsTrue(sbf.IsSubgraph());
Assert.AreEqual(24, sbf.GetAllAtomMapping().Count);
}
public void TestSMSDCyclohexaneBenzeneSubgraph()
{
// IQueryAtomContainer queryContainer = QueryAtomContainerCreator.CreateSymbolAndBondOrderQueryContainer(Cyclohexane);
Isomorphism ebimcs = new Isomorphism(Algorithm.VFLibMCS, true);
ebimcs.Init(Cyclohexane, Benzene, true, true);
ebimcs.SetChemFilters(true, true, true);
Assert.IsFalse(ebimcs.IsSubgraph());
}
public void TestIsSubgraph()
{
var sp = CDK.SmilesParser;
var target = sp.ParseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
var queryac = sp.ParseSmiles("Nc1ccccc1");
Isomorphism smsd1 = new Isomorphism(Algorithm.SubStructure, false);
smsd1.Init(queryac, target, true, true);
smsd1.SetChemFilters(true, true, true);
Assert.AreEqual(true, smsd1.IsSubgraph());
}
public void TestSetChemFilters()
{
var sp = CDK.SmilesParser;
var target = sp.ParseSmiles("C\\C=C/OCC=C");
var queryac = sp.ParseSmiles("CCCOCC(C)=C");
Isomorphism smsd1 = new Isomorphism(Algorithm.Default, false);
smsd1.Init(queryac, target, true, true);
smsd1.SetChemFilters(true, true, true);
Assert.AreEqual(1, smsd1.GetAllAtomMapping().Count);
}
public void TestSet_IAtomContainer_IAtomContainer()
{
var sp = CDK.SmilesParser;
var target = sp.ParseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
var queryac = sp.ParseSmiles("Nc1ccccc1");
Isomorphism smsd1 = new Isomorphism(Algorithm.Default, true);
smsd1.Init(queryac, target, true, true);
smsd1.SetChemFilters(true, true, true);
Assert.IsNotNull(smsd1.GetFirstMapping());
}
public void TestInit_3args_2()
{
var sp = CDK.SmilesParser;
var target = sp.ParseSmiles("C\\C=C/OCC=C");
var queryac = sp.ParseSmiles("CCCOCC(C)=C");
Isomorphism smsd1 = new Isomorphism(Algorithm.Default, false);
smsd1.Init(queryac, target, true, true);
smsd1.SetChemFilters(true, false, false);
Assert.IsNotNull(smsd1.ReactantMolecule);
Assert.IsNotNull(smsd1.ProductMolecule);
}
public void TestGetProductMolecule()
{
var sp = CDK.SmilesParser;
var target = sp.ParseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
var queryac = sp.ParseSmiles("Nc1ccccc1");
Isomorphism smsd1 = new Isomorphism(Algorithm.Default, true);
smsd1.Init(queryac, target, true, true);
smsd1.SetChemFilters(true, true, true);
Assert.AreEqual(20, smsd1.ProductMolecule.Atoms.Count);
}
public void TestSet_MolHandler_MolHandler()
{
var sp = CDK.SmilesParser;
var target1 = sp.ParseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
var queryac = sp.ParseSmiles("Nc1ccccc1");
MolHandler source = new MolHandler(queryac, true, true);
MolHandler target = new MolHandler(target1, true, true);
Isomorphism smsd1 = new Isomorphism(Algorithm.Default, true);
smsd1.Init(source.Molecule, target.Molecule, true, true);
smsd1.SetChemFilters(true, true, true);
Assert.IsNotNull(smsd1.GetFirstMapping());
}
public void TestGetStereoScore()
{
var sp = CDK.SmilesParser;
var target = sp.ParseSmiles("C\\C=C/OCC=C");
var queryac = sp.ParseSmiles("CCCOCC(C)=C");
Isomorphism smsd1 = new Isomorphism(Algorithm.Default, false);
smsd1.Init(queryac, target, true, true);
smsd1.SetChemFilters(true, false, false);
int score = 1048;
Assert.AreEqual(score, smsd1.GetStereoScore(0));
}
public void TestGetEnergyScore()
{
var sp = CDK.SmilesParser;
var target = sp.ParseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
var queryac = sp.ParseSmiles("Nc1ccccc1");
Isomorphism smsd1 = new Isomorphism(Algorithm.Default, true);
smsd1.Init(queryac, target, true, true);
smsd1.SetChemFilters(false, false, true);
double score = 610.0;
Assert.AreEqual(score, smsd1.GetEnergyScore(0));
}
public void TestSMSDBondInSensitive()
{
Isomorphism ebimcs1 = new Isomorphism(Algorithm.Default, false);
ebimcs1.Init(Cyclohexane, Benzene, true, true);
ebimcs1.SetChemFilters(true, true, true);
Assert.AreEqual(6, ebimcs1.GetFirstAtomMapping().Count);
Isomorphism ebimcs2 = new Isomorphism(Algorithm.Default, false);
ebimcs2.Init(Benzene, Napthalene, true, true);
ebimcs2.SetChemFilters(true, true, true);
Assert.AreEqual(6, ebimcs2.GetFirstAtomMapping().Count);
}
public void TestGetTanimotoSimilarity()
{
var sp = CDK.SmilesParser;
var target = sp.ParseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
var queryac = sp.ParseSmiles("Nc1ccccc1");
Isomorphism smsd1 = new Isomorphism(Algorithm.Default, true);
smsd1.Init(queryac, target, true, true);
smsd1.SetChemFilters(true, true, true);
double score = 0.35;
Assert.AreEqual(score, smsd1.GetTanimotoSimilarity(), 0);
}
public void TestGetEuclideanDistance()
{
var sp = CDK.SmilesParser;
var target = sp.ParseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
var queryac = sp.ParseSmiles("Nc1ccccc1");
var smsd1 = new Isomorphism(Algorithm.SubStructure, true);
smsd1.Init(queryac, target, true, true);
smsd1.SetChemFilters(true, true, true);
double score = 3.605;
Assert.AreEqual(score, smsd1.GetEuclideanDistance(), 0.005);
Isomorphism smsd2 = new Isomorphism(Algorithm.VFLibMCS, true);
smsd2.Init(queryac, target, true, true);
smsd2.SetChemFilters(true, true, true);
Assert.AreEqual(score, smsd2.GetEuclideanDistance(), 0.005);
}
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 TestSMSDBondSensitive()
{
Isomorphism ebimcs3 = new Isomorphism(Algorithm.CDKMCS, true);
ebimcs3.Init(Cyclohexane, Benzene, true, true);
ebimcs3.SetChemFilters(false, false, false);
Assert.IsFalse(ebimcs3.IsSubgraph());
Isomorphism ebimcs4 = new Isomorphism(Algorithm.CDKMCS, true);
ebimcs4.Init(Benzene, Napthalene, true, true);
ebimcs4.SetChemFilters(true, true, true);
Assert.AreEqual(6, ebimcs4.GetFirstAtomMapping().Count);
Isomorphism ebimcs5 = new Isomorphism(Algorithm.VFLibMCS, true);
ebimcs5.Init(Cyclohexane, Benzene, true, true);
ebimcs5.SetChemFilters(true, true, true);
Assert.IsFalse(ebimcs5.IsSubgraph());
Isomorphism ebimcs6 = new Isomorphism(Algorithm.VFLibMCS, true);
ebimcs6.Init(Benzene, Napthalene, true, true);
ebimcs6.SetChemFilters(true, true, true);
Assert.AreEqual(6, ebimcs6.GetFirstAtomMapping().Count);
Isomorphism ebimcs7 = new Isomorphism(Algorithm.MCSPlus, true);
ebimcs7.Init(Cyclohexane, Benzene, true, true);
ebimcs7.SetChemFilters(true, true, true);
Assert.IsFalse(ebimcs7.IsSubgraph());
Isomorphism ebimcs8 = new Isomorphism(Algorithm.MCSPlus, true);
ebimcs8.Init(Benzene, Napthalene, true, true);
ebimcs8.SetChemFilters(true, true, true);
Assert.AreEqual(6, ebimcs8.GetFirstAtomMapping().Count);
}
public void TestSet_String_String()
{
string molfile = "NCDK.Data.MDL.decalin.mol";
string queryfile = "NCDK.Data.MDL.decalin.mol";
IAtomContainer query = new AtomContainer();
IAtomContainer target = new AtomContainer();
var ins = ResourceLoader.GetAsStream(molfile);
var reader = new MDLV2000Reader(ins, ChemObjectReaderMode.Strict);
reader.Read(query);
ins = ResourceLoader.GetAsStream(queryfile);
reader = new MDLV2000Reader(ins, ChemObjectReaderMode.Strict);
reader.Read(target);
Isomorphism smsd1 = new Isomorphism(Algorithm.Default, true);
smsd1.Init(query, target, true, true);
smsd1.SetChemFilters(true, true, true);
double score = 1.0;
Assert.AreEqual(score, smsd1.GetTanimotoSimilarity(), 0.0001);
}
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);
}