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 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 TestGetFirstAtomMapping()
{
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(7, smsd1.GetFirstAtomMapping().Count);
}
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.SubStructure, false);
smsd1.Init(queryac, target, true, true);
smsd1.SetChemFilters(false, false, true);
var score = 610.0;
Assert.AreEqual(score, smsd1.GetEnergyScore(0));
}
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 TestGetSortedFragment()
{
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, true, false);
int score = 2;
Assert.AreEqual(score, smsd1.GetFragmentSize(0));
}
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 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);
Isomorphism smsd1 = new Isomorphism(Algorithm.Default, true);
smsd1.Init(queryac, target, true, true);
smsd1.SetChemFilters(true, true, true);
Assert.AreEqual(2, smsd1.GetAllAtomMapping().Count);
}
public void TestSortResultsByEnergies()
{
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 smsd = new Isomorphism(Algorithm.Default, true);
smsd.Init(queryac, target, true, true);
smsd.SetChemFilters(false, false, false);
Assert.AreEqual(4, smsd.GetAllAtomMapping().Count);
Isomorphism smsd1 = new Isomorphism(Algorithm.Default, true);
smsd1.Init(queryac, target, true, true);
smsd1.SetChemFilters(false, false, true);
Assert.AreEqual(2, smsd1.GetAllAtomMapping().Count);
}
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");
Isomorphism 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 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);
}