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 BiDirectionLookup()
{
var x = new Isomorphism <string, int>
{
{ "I", 1 },
{ "V", 5 }
};
x["V"].ShouldBe(5);
x[5].ShouldBe("V");
x["I"].ShouldBe(1);
x[1].ShouldBe("I");
}
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 Creation()
{
var x = new Isomorphism <int, int>
{
{ 1, 2 },
{ 2, 4 }
};
var y = new Isomorphism <string, int>
{
{ "I", 1 },
{ "V", 5 }
};
}
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);
}
public RomanNumerableTests()
{
_simpleMappings = new Isomorphism <string, int>
{
{ "I", 1 },
{ "II", 2 },
{ "III", 3 },
{ "V", 5 },
{ "VI", 6 },
{ "X", 10 },
{ "XI", 11 },
{ "XVI", 16 },
{ "XX", 20 },
{ "XXI", 21 },
{ "XXII", 22 },
{ "XXV", 25 },
{ "XXXVII", 37 },
{ "L", 50 },
{ "LI", 51 },
{ "LV", 55 },
{ "LX", 60 },
{ "LXXXVII", 87 },
{ "CI", 101 },
{ "CV", 105 },
{ "CX", 110 },
{ "CL", 150 },
{ "CLX", 160 },
{ "CLXXVII", 177 },
{ "CC", 200 },
{ "CCCLXXVII", 377 },
{ "D", 500 },
{ "DI", 501 },
{ "DV", 505 },
{ "DX", 510 },
{ "DL", 550 },
{ "DC", 600 },
{ "DCCCLXXXVI", 886 },
{ "M", 1000 },
{ "MI", 1001 },
{ "MV", 1005 },
{ "MX", 1010 },
{ "ML", 1050 },
{ "MD", 1500 },
{ "MM", 2000 },
{ "MMDCCLXVII", 2767 },
{ "MDCVI", 1606 },
{ "MMMMMMMDCCCLXI", 7861 }
};
_subtraciveMappings = new Isomorphism <string, int>
{
{ "IV", 4 },
{ "IX", 9 },
{ "XIV", 14 },
{ "XIX", 19 },
{ "XXIV", 24 },
{ "XXIX", 29 },
{ "XL", 40 },
{ "XLIV", 44 },
{ "XLIX", 49 },
{ "XC", 90 },
{ "XCIV", 94 },
{ "XCIX", 99 },
{ "CD", 400 },
{ "CDXLIV", 444 },
{ "CM", 900 },
{ "CMXCIX", 999 },
{ "MMMMCDXCI", 4491 }
};
}
