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 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 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 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 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 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 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 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 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 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 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 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 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 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 TestImpossibleQuery()
{
Isomorphism smsd = new Isomorphism(Algorithm.Default, true);
var sp = CDK.SmilesParser;
var query = sp.ParseSmiles("CC");
var target = sp.ParseSmiles("C");
smsd.Init(query, target, false, true);
bool foundMatches = smsd.IsSubgraph();
Assert.IsFalse(foundMatches);
}
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 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 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 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 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 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 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 TestQueryAtomContainerMCSPLUS()
{
Isomorphism smsd = new Isomorphism(Algorithm.MCSPlus, true);
var sp = CDK.SmilesParser;
var query = sp.ParseSmiles("CC");
var target = sp.ParseSmiles("C1CCC12CCCC2");
smsd.Init(query, target, false, true);
bool foundMatches = smsd.IsSubgraph();
Assert.IsTrue(foundMatches);
IQueryAtomContainer queryContainer = QueryAtomContainerCreator.CreateSymbolAndBondOrderQueryContainer(query);
smsd.Init(queryContainer, target);
foundMatches = smsd.IsSubgraph();
Assert.IsTrue(foundMatches);
}
public void TestMatchCountCDKMCS()
{
Isomorphism smsd = new Isomorphism(Algorithm.CDKMCS, true);
var sp = CDK.SmilesParser;
var query = sp.ParseSmiles("CC");
var target = sp.ParseSmiles("C1CCC12CCCC2");
smsd.Init(query, target, false, true);
bool foundMatches = smsd.IsSubgraph();
Assert.AreEqual(18, smsd.GetAllAtomMapping().Count);
Assert.IsTrue(foundMatches);
IQueryAtomContainer queryContainer = QueryAtomContainerCreator.CreateSymbolAndBondOrderQueryContainer(query);
smsd.Init(queryContainer, target);
foundMatches = smsd.IsSubgraph();
Assert.IsTrue(foundMatches);
}
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);
}