public void TestBasicAmineOnDrugs()
{
var filename = "drugs.smi";
var ins = ResourceLoader.GetAsStream(GetType(), filename);
SMARTSQueryTool sqt = new SMARTSQueryTool("[NX3;H2,H1;!$(NC=O)]", ChemObjectBuilder.Instance);
// iterating SMILES reader doesn't allow us to turn off automatic aromaticity
// perception
var sp = CDK.SmilesParser;
int nmatch = 0;
int nmol = 0;
using (var reader = new StreamReader(ins))
{
string smi;
while ((smi = reader.ReadLine()) != null)
{
var container = sp.ParseSmiles(smi.Split('\t')[0]);
if (sqt.Matches(container))
{
nmatch++;
}
nmol++;
}
Assert.AreEqual(141, nmol);
Assert.AreEqual(0, nmatch);
}
}
public void TestRecursive29()
{
SMARTSQueryTool sqt = CreateFromSmarts("[NX3;H2,H1;!$(NC=O)]");
IAtomContainer smi = CreateFromSmiles("Cc1cc(=O)c(c[nH]1)C(=O)NC(c1ccc(cc1)O)C(=O)NC1C(=O)N2C1SCC(=C2C(=O)O)CSc1nnnn1C");
int[] result = SMARTSSearchTest.Match(sqt, smi);
Assert.AreEqual(0, result[0]);
Assert.AreEqual(0, result[1]);
}
public void TestRecursive28()
{
SMARTSQueryTool sqt = CreateFromSmarts("[NX3;H2,H1;!$(NC=O)]");
IAtomContainer smi = CreateFromSmiles("Cc1ccc[n+]2c1[nH]cc(c2=O)c1n[nH]nn1");
int[] result = SMARTSSearchTest.Match(sqt, smi);
Assert.AreEqual(0, result[0]);
Assert.AreEqual(0, result[1]);
}
public void TestRecursiveSmarts27()
{
SMARTSQueryTool sqt = CreateFromSmarts("[NX3;H2,H1;!$(NC=O)]");
IAtomContainer smi = CreateFromSmiles("CCCc1nc(c2n1[nH]c(nc2=O)c1cc(ccc1OCC)S(=O)(=O)N1CCN(CC1)CC)C");
int[] result = SMARTSSearchTest.Match(sqt, smi);
Assert.AreEqual(0, result[0]);
Assert.AreEqual(0, result[1]);
}
public void TestRecursiveSmarts26()
{
SMARTSQueryTool sqt = CreateFromSmarts("[NX3;H2,H1;!$(NC=O)]");
IAtomContainer smi = CreateFromSmiles("CCCc1cc(=O)nc([nH]1)S");
int[] result = SMARTSSearchTest.Match(sqt, smi);
Assert.AreEqual(0, result[0]);
Assert.AreEqual(0, result[1]);
}
public void TestRecursive29_cdkAromaticModel()
{
SMARTSQueryTool sqt = CreateFromSmarts("[NX3;H2,H1;!$(NC=O)]");
IAtomContainer smi = CreateFromSmiles("Cc1cc(=O)c(c[nH]1)C(=O)NC(c1ccc(cc1)O)C(=O)NC1C(=O)N2C1SCC(=C2C(=O)O)CSc1nnnn1C");
sqt.SetAromaticity(new Aromaticity(ElectronDonation.CDKModel, Cycles.CDKAromaticSetFinder));
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(smi);
int[] result = SMARTSSearchTest.Match(sqt, smi);
Assert.AreEqual(1, result[0]);
Assert.AreEqual(1, result[1]);
}
public void TestRecursiveSmarts27_cdkAromaticModel()
{
SMARTSQueryTool sqt = CreateFromSmarts("[NX3;H2,H1;!$(NC=O)]");
IAtomContainer smi = CreateFromSmiles("CCCc1nc(c2n1[nH]c(nc2=O)c1cc(ccc1OCC)S(=O)(=O)N1CCN(CC1)CC)C");
sqt.SetAromaticity(new Aromaticity(ElectronDonation.CDKModel, Cycles.CDKAromaticSetFinder));
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(smi);
int[] result = SMARTSSearchTest.Match(sqt, smi);
Assert.AreEqual(1, result[0]);
Assert.AreEqual(1, result[1]);
}
public void Match(string smarts, string smiles)
{
SMARTSQueryTool sqt = new SMARTSQueryTool(smarts, ChemObjectBuilder.Instance);
var sp = CDK.SmilesParser;
var atomContainer = sp.ParseSmiles(smiles);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(atomContainer);
Aromaticity.CDKLegacy.Apply(atomContainer);
bool status = sqt.Matches(atomContainer);
if (status)
{
nmatch = sqt.MatchesCount;
nqmatch = sqt.GetUniqueMatchingAtoms().Count();
}
else
{
nmatch = 0;
nqmatch = 0;
}
}
public void TestBasicAmineOnDrugs_cdkAromaticModel()
{
var filename = "drugs.smi";
var ins = ResourceLoader.GetAsStream(GetType(), filename);
using (EnumerableSMILESReader reader = new EnumerableSMILESReader(ins, ChemObjectBuilder.Instance))
{
SMARTSQueryTool sqt = new SMARTSQueryTool("[NX3;H2,H1;!$(NC=O)]", ChemObjectBuilder.Instance);
sqt.SetAromaticity(new Aromaticity(ElectronDonation.CDKModel, Cycles.CDKAromaticSetFinder));
int nmatch = 0;
int nmol = 0;
foreach (var container in reader)
{
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(container);
// skip un-typed atoms, they can't be run through the CDK aromatic
// model
foreach (var atom in container.Atoms)
{
if (atom.AtomTypeName == null)
{
goto continue_READ;
}
}
if (sqt.Matches(container))
{
nmatch++;
}
nmol++;
continue_READ:
;
}
Assert.AreEqual(141, nmol);
Assert.AreEqual(4, nmatch);
}
}
static void AssertMatch(SMARTSQueryTool sqt, IAtomContainer m, int hits, int usaHits)
{
sqt.Matches(m);
Assert.AreEqual(hits, sqt.GetMatchingAtoms().Count());
Assert.AreEqual(usaHits, sqt.GetUniqueMatchingAtoms().Count());
}
