public void TestSingleAtomMatching2()
{
var sp = CDK.SmilesParser;
var target = sp.ParseSmiles("CNC");
var queryac = sp.ParseSmiles("C");
var query = QueryAtomContainerCreator.CreateSymbolAndBondOrderQueryContainer(queryac);
var matches = uiTester.GetIsomorphMaps(target, query).ToReadOnlyList();
Assert.AreEqual(2, matches.Count);
Assert.AreEqual(1, matches[0].Count);
Assert.AreEqual(1, matches[1].Count);
var map1 = matches[0][0];
var map2 = matches[1][0];
Assert.AreEqual(0, map1.Id1);
Assert.AreEqual(0, map1.Id2);
Assert.AreEqual(2, map2.Id1);
Assert.AreEqual(0, map2.Id2);
var atomMappings = UniversalIsomorphismTester.MakeAtomsMapsOfBondsMaps(matches, target, query);
Assert.IsTrue(Compares.AreDeepEqual(matches, atomMappings));
}
public void TestSingleAtomMatching2()
{
var sp = CDK.SmilesParser;
var target = sp.ParseSmiles("CNC");
var queryac = sp.ParseSmiles("C");
var query = QueryAtomContainerCreator.CreateSymbolAndBondOrderQueryContainer(queryac);
var matches = CDKMCS.GetIsomorphMaps(target, query, true);
Assert.AreEqual(2, matches.Count);
Assert.AreEqual(1, matches[0].Count);
Assert.AreEqual(1, matches[1].Count);
var map1 = matches[0][0];
var map2 = matches[1][0];
Assert.AreEqual(0, map1.Id1);
Assert.AreEqual(0, map1.Id2);
Assert.AreEqual(2, map2.Id1);
Assert.AreEqual(0, map2.Id2);
var atomMappings = CDKMCS.MakeAtomsMapsOfBondsMaps(matches, target, query);
Assert.AreEqual(matches, atomMappings);
}
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);
}
/// <summary>
/// Search if the setOfAtomContainer contains the atomContainer
/// </summary>
/// <param name="set">ISetOfAtomContainer object where to search</param>
/// <param name="atomContainer">IAtomContainer to search</param>
/// <returns>True, if the atomContainer is contained</returns>
private bool ExistAC(IChemObjectSet <IAtomContainer> set, IAtomContainer atomContainer)
{
IAtomContainer acClone = null;
acClone = (IAtomContainer)atomContainer.Clone();
if (!lookingSymmetry)
{ /* remove all aromatic flags */
foreach (var atom in acClone.Atoms)
{
atom.IsAromatic = false;
}
foreach (var bond in acClone.Bonds)
{
bond.IsAromatic = false;
}
}
for (int i = 0; i < acClone.Atoms.Count; i++)
{
acClone.Atoms[i].Id = "" + acClone.Atoms.IndexOf(acClone.Atoms[i]);
}
if (lookingSymmetry)
{
try
{
Aromaticity.CDKLegacy.Apply(acClone);
}
catch (CDKException e)
{
Console.Error.WriteLine(e.StackTrace);
}
}
else
{
if (!lookingSymmetry)
{ /* remove all aromatic flags */
foreach (var atom in acClone.Atoms)
{
atom.IsAromatic = false;
}
foreach (var bond in acClone.Bonds)
{
bond.IsAromatic = false;
}
}
}
for (int i = 0; i < set.Count; i++)
{
var ss = set[i];
for (int j = 0; j < ss.Atoms.Count; j++)
{
ss.Atoms[j].Id = "" + ss.Atoms.IndexOf(ss.Atoms[j]);
}
try
{
if (!lookingSymmetry)
{
var qAC = QueryAtomContainerCreator.CreateSymbolChargeIDQueryContainer(acClone);
if (new UniversalIsomorphismTester().IsIsomorph(ss, qAC))
{
var qAC2 = QueryAtomContainerCreator.CreateSymbolAndBondOrderQueryContainer(acClone);
if (new UniversalIsomorphismTester().IsIsomorph(ss, qAC2))
{
return(true);
}
}
}
else
{
var qAC = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(acClone);
Aromaticity.CDKLegacy.Apply(ss);
if (new UniversalIsomorphismTester().IsIsomorph(ss, qAC))
{
return(true);
}
}
}
catch (CDKException e1)
{
Console.Error.WriteLine(e1);
Trace.TraceError(e1.Message);
Debug.WriteLine(e1);
}
}
return(false);
}
