public void TestQueryToolReSetSmarts()
{
var sp = CDK.SmilesParser;
var atomContainer = sp.ParseSmiles("C1CCC12CCCC2");
SMARTSQueryTool querytool = new SMARTSQueryTool("C", ChemObjectBuilder.Instance);
bool status = querytool.Matches(atomContainer);
Assert.IsTrue(status);
int nmatch = querytool.MatchesCount;
Assert.AreEqual(8, nmatch);
querytool.Smarts = "CC";
status = querytool.Matches(atomContainer);
Assert.IsTrue(status);
nmatch = querytool.MatchesCount;
Assert.AreEqual(18, nmatch);
var umatch = querytool.GetUniqueMatchingAtoms();
Assert.AreEqual(9, umatch.Count());
}
static void Main()
{
{
#region
SmilesParser sp = new SmilesParser();
IAtomContainer atomContainer = sp.ParseSmiles("CC(=O)OC(=O)C");
SMARTSQueryTool querytool = new SMARTSQueryTool("O=CO");
bool status = querytool.Matches(atomContainer);
if (status)
{
int nmatch = querytool.MatchesCount;
var mappings = querytool.GetMatchingAtoms();
foreach (var atomIndices in mappings)
{
// do something
}
}
#endregion
}
{
string someSmartsPattern = null;
IChemObjectSet <IAtomContainer> molecules = null;
#region SetAromaticity
SMARTSQueryTool sqt = new SMARTSQueryTool(someSmartsPattern);
sqt.SetAromaticity(new Aromaticity(ElectronDonation.CDKModel, Cycles.CDKAromaticSetFinder));
foreach (var molecule in molecules)
{
// CDK Aromatic model needs atom types
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
sqt.Matches(molecule);
}
#endregion
}
}
public void TestMethane()
{
IAtomContainer methane = CDK.Builder.NewAtomContainer();
IAtom carbon = methane.Builder.NewAtom(ChemicalElement.C);
carbon.ImplicitHydrogenCount = 4;
methane.Atoms.Add(carbon);
SMARTSQueryTool sqt = new SMARTSQueryTool("CC", ChemObjectBuilder.Instance);
bool matches = sqt.Matches(methane);
Assert.IsFalse(matches);
}
public void TestQueryToolSingleAtomCase()
{
var sp = CDK.SmilesParser;
var atomContainer = sp.ParseSmiles("C1CCC12CCCC2");
SMARTSQueryTool querytool = new SMARTSQueryTool("C", ChemObjectBuilder.Instance);
bool status = querytool.Matches(atomContainer);
Assert.IsTrue(status);
int nmatch = querytool.MatchesCount;
Assert.AreEqual(8, nmatch);
}
public void SetAromaticity()
{
SMARTSQueryTool sqt = new SMARTSQueryTool("[a]", ChemObjectBuilder.Instance);
IAtomContainer furan = CreateFromSmiles("O1C=CC=C1");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(furan);
sqt.SetAromaticity(new Aromaticity(ElectronDonation.CDKModel, Cycles.MCBFinder));
Assert.IsTrue(sqt.Matches(furan, true));
sqt.SetAromaticity(new Aromaticity(ElectronDonation.PiBondsModel, Cycles.MCBFinder));
Assert.IsFalse(sqt.Matches(furan, true));
}
public void TestIndoleAgainstItself()
{
IAtomContainer indole = TestMoleculeFactory.MakeIndole();
AddImplicitHydrogens(indole);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(indole);
Aromaticity.CDKLegacy.Apply(indole);
SmilesGenerator generator = new SmilesGenerator().Aromatic();
string indoleSmiles = generator.Create(indole);
var smilesParser = CDK.SmilesParser;
indole = smilesParser.ParseSmiles(indoleSmiles);
SMARTSQueryTool querytool = new SMARTSQueryTool(indoleSmiles, ChemObjectBuilder.Instance);
Assert.IsTrue(querytool.Matches(indole));
}
public void TestQuery()
{
var sp = CDK.SmilesParser;
var atomContainer = sp.ParseSmiles("c12cc(CCN)ccc1c(COC)ccc2");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(atomContainer);
Aromaticity.CDKLegacy.Apply(atomContainer);
SMARTSQueryTool querytool = new SMARTSQueryTool("c12ccccc1cccc2", ChemObjectBuilder.Instance);
bool status = querytool.Matches(atomContainer);
Assert.IsTrue(status);
int nmatch = querytool.MatchesCount;
Assert.AreEqual(4, nmatch);
var umatch = querytool.GetUniqueMatchingAtoms();
Assert.AreEqual(1, umatch.Count());
}
public void TestUniqueQueries()
{
var sp = CDK.SmilesParser;
var atomContainer = sp.ParseSmiles("c1ccccc1CCCNCCCc1ccccc1");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(atomContainer);
Aromaticity.CDKLegacy.Apply(atomContainer);
SMARTSQueryTool querytool = new SMARTSQueryTool("c1ccccc1");
bool status = querytool.Matches(atomContainer);
Assert.IsTrue(status);
int nmatch = querytool.MatchesCount;
Assert.AreEqual(24, nmatch);
var umatch = querytool.GetUniqueMatchingAtoms();
Assert.AreEqual(2, umatch.Count());
}
public void TestQueryTool()
{
var sp = CDK.SmilesParser;
var atomContainer = sp.ParseSmiles("CC(=O)OC(=O)C");
SMARTSQueryTool querytool = new SMARTSQueryTool("O=CO", ChemObjectBuilder.Instance);
bool status = querytool.Matches(atomContainer);
Assert.IsTrue(status);
int nmatch = querytool.MatchesCount;
Assert.AreEqual(2, nmatch);
List <int> map1 = new List <int> {
1, 2, 3,
};
List <int> map2 = new List <int> {
3, 4, 5,
};
var mappings = querytool.GetMatchingAtoms().ToReadOnlyList();
var ret1 = mappings[0].OrderBy(n => n).ToReadOnlyList();
for (int i = 0; i < 3; i++)
{
Assert.IsTrue(Compares.AreDeepEqual(map1[i], ret1[i]));
}
var ret2 = mappings[1].OrderBy(n => n).ToReadOnlyList();
for (int i = 0; i < 3; i++)
{
Assert.AreEqual(map2[i], ret2[i]);
}
}
public void TestLexicalError()
{
SMARTSQueryTool sqt = new SMARTSQueryTool("Epoxide", ChemObjectBuilder.Instance);
}
public void NullAromaticity()
{
SMARTSQueryTool sqt = new SMARTSQueryTool("CC", ChemObjectBuilder.Instance);
sqt.SetAromaticity(null);
}
public void TestLexicalError()
{
SMARTSQueryTool sqt = new SMARTSQueryTool("Epoxide");
}
public void NullAromaticity()
{
SMARTSQueryTool sqt = new SMARTSQueryTool("CC");
sqt.SetAromaticity(null);
}