public void TestRgroupQueryFile3()
{
var filename = "NCDK.Data.MDL.rgfile.3.mol";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
RGroupQueryReader reader = new RGroupQueryReader(ins);
RGroupQuery rGroupQuery = (RGroupQuery)reader.Read(new RGroupQuery(ChemObjectBuilder.Instance));
reader.Close();
Assert.IsNotNull(rGroupQuery);
Assert.AreEqual(rGroupQuery.RGroupDefinitions.Count, 1);
Assert.AreEqual(rGroupQuery.RootStructure.Atoms.Count, 10);
Assert.AreEqual(rGroupQuery.RootAttachmentPoints.Count, 2);
Assert.AreEqual(rGroupQuery.GetAllConfigurations().Count(), 8);
//Test correctness AAL lines
foreach (var at in rGroupQuery.GetRgroupQueryAtoms(1))
{
if (at is PseudoAtom)
{
Assert.AreEqual(((PseudoAtom)at).Label, "R1");
var apoBonds = rGroupQuery.RootAttachmentPoints[at];
Assert.AreEqual(apoBonds.Count, 2);
var boundAtom1 = apoBonds[1].GetOther(at);
Assert.IsTrue(boundAtom1.Symbol.Equals("Te") || boundAtom1.Symbol.Equals("S"));
var boundAtom2 = apoBonds[2].GetOther(at);
Assert.IsTrue(boundAtom2.Symbol.Equals("Po") || boundAtom2.Symbol.Equals("O"));
}
}
// Test that there only two Rgroup query atoms (R#). The third R is a
// pseudo atom, but because it is not numbered it is not part of any
// query condition.
var allrGroupQueryAtoms = rGroupQuery.GetAllRgroupQueryAtoms();
Assert.AreEqual(allrGroupQueryAtoms.Count, 2);
}
public void TestRgroupQueryFile1()
{
var filename = "NCDK.Data.MDL.rgfile.1.mol";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
RGroupQueryReader reader = new RGroupQueryReader(ins);
RGroupQuery rGroupQuery = (RGroupQuery)reader.Read(new RGroupQuery(ChemObjectBuilder.Instance));
reader.Close();
Assert.IsNotNull(rGroupQuery);
Assert.AreEqual(rGroupQuery.RGroupDefinitions.Count, 1);
Assert.AreEqual(rGroupQuery.RootStructure.Atoms.Count, 7);
foreach (var at in rGroupQuery.GetAllRgroupQueryAtoms())
{
if (at is PseudoAtom)
{
Assert.AreEqual(((PseudoAtom)at).Label, "R1");
var rootApo = rGroupQuery.RootAttachmentPoints;
var apoBonds = rootApo[at];
Assert.AreEqual(apoBonds.Count, 1);
// Assert that the root attachment is the bond between R1 and P
foreach (var bond in rGroupQuery.RootStructure.Bonds)
{
if (bond.Contains(at))
{
Assert.AreEqual(bond, apoBonds[1]);
foreach (var atInApo in bond.Atoms)
{
Assert.IsTrue(atInApo.Symbol.Equals("R") || atInApo.Symbol.Equals("P"));
}
}
}
}
}
int val_1 = rGroupQuery.RGroupDefinitions.Keys.First();
Assert.AreEqual(val_1, 1);
RGroupList rList = rGroupQuery.RGroupDefinitions[val_1];
Assert.AreEqual(rList.Occurrence, "0,1-3");
var rGroups = rList.RGroups;
Assert.AreEqual(rGroups[0].FirstAttachmentPoint.Symbol, "N");
Assert.AreEqual(rGroups[1].FirstAttachmentPoint.Symbol, "O");
Assert.AreEqual(rGroups[2].FirstAttachmentPoint.Symbol, "S");
Assert.IsNull(rGroups[0].SecondAttachmentPoint);
Assert.IsNull(rGroups[1].SecondAttachmentPoint);
Assert.IsNull(rGroups[2].SecondAttachmentPoint);
var configurations = rGroupQuery.GetAllConfigurations();
Assert.AreEqual(configurations.Count(), 4);
//IsRestH is set to true for R1, so with zero substitutes, the phosphor should get the restH flag set to true.
bool restH_Identified = false;
foreach (var atc in configurations)
{
if (atc.Atoms.Count == 6)
{
foreach (var atom in atc.Atoms)
{
if (atom.Symbol.Equals("P"))
{
Assert.IsNotNull(atom.GetProperty <bool?>(CDKPropertyName.RestH));
Assert.AreEqual(atom.GetProperty <bool>(CDKPropertyName.RestH), true);
restH_Identified = true;
}
}
}
}
Assert.IsTrue(restH_Identified);
}