public void TestRgroupQueryFile4()
{
var filename = "NCDK.Data.MDL.rgfile.4.mol";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new RGroupQueryReader(ins);
var 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, 6);
var allrGroupQueryAtoms = rGroupQuery.GetAllRgroupQueryAtoms();
Assert.AreEqual(allrGroupQueryAtoms.Count, 1);
var rList = rGroupQuery.RGroupDefinitions[1];
Assert.AreEqual(rList.RGroups.Count, 2);
Assert.AreEqual(rList.RequiredRGroupNumber, 0);
Assert.IsFalse(rList.IsRestH);
Assert.AreEqual(rGroupQuery.RootAttachmentPoints.Count, 0);
Assert.IsTrue(rGroupQuery.AreSubstituentsDefined());
Assert.AreEqual(rGroupQuery.GetAllConfigurations().Count(), 2);
// This query has a detached R-group, test for empty attachment points
var rGroups = rList.RGroups;
Assert.AreEqual(rGroups[0].FirstAttachmentPoint, null);
Assert.AreEqual(rGroups[0].SecondAttachmentPoint, null);
Assert.AreEqual(rGroups[1].FirstAttachmentPoint, null);
Assert.AreEqual(rGroups[1].SecondAttachmentPoint, null);
}
public void TestAccepts()
{
RGroupQueryReader reader = new RGroupQueryReader(new StringReader(""));
Assert.IsFalse(reader.Accepts(typeof(AtomContainer)));
Assert.IsTrue(reader.Accepts(typeof(RGroupQuery)));
}
private string Recreate(string file)
{
StringWriter sw = new StringWriter();
RGroupQueryWriter rgw = new RGroupQueryWriter(sw);
var ins = ResourceLoader.GetAsStream(file);
RGroupQueryReader reader = new RGroupQueryReader(ins);
RGroupQuery rGroupQuery = (RGroupQuery)reader.Read(new RGroupQuery());
rgw.Write(rGroupQuery);
string output = sw.ToString();
return(output);
}
public void TestRgroupQueryFile7()
{
var filename = "NCDK.Data.MDL.rgfile.7.mol";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new RGroupQueryReader(ins);
var rGroupQuery = reader.Read(new RGroupQuery(ChemObjectBuilder.Instance));
reader.Close();
Assert.IsNotNull(rGroupQuery);
Assert.AreEqual(rGroupQuery.RGroupDefinitions.Count, 1);
Assert.AreEqual(rGroupQuery.RootStructure.Atoms.Count, 9);
Assert.AreEqual(rGroupQuery.GetAllConfigurations().Count(), 20);
}
public void TestRgroupQueryFile5()
{
var filename = "NCDK.Data.MDL.rgfile.5.mol";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new RGroupQueryReader(ins);
var rGroupQuery = reader.Read(new RGroupQuery(ChemObjectBuilder.Instance));
reader.Close();
Assert.IsNotNull(rGroupQuery);
Assert.AreEqual(rGroupQuery.RGroupDefinitions.Count, 4);
//Test combinatorial explosion: R5 has many different configurations
Assert.AreEqual(rGroupQuery.GetAllConfigurations().Count(), 17820);
}
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 TestRgroupQueryFile6()
{
var filename = "NCDK.Data.MDL.rgfile.6.mol";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new RGroupQueryReader(ins);
var rGroupQuery = (RGroupQuery)reader.Read(new RGroupQuery(ChemObjectBuilder.Instance));
reader.Close();
Assert.IsNotNull(rGroupQuery);
Assert.AreEqual(rGroupQuery.RGroupDefinitions.Count, 3);
Assert.AreEqual(rGroupQuery.RootStructure.Atoms.Count, 14);
// This file has missing $RGP blocks. You could argue that this is
// thus not a legal query (ie missing query specifications)
Assert.IsFalse(rGroupQuery.AreSubstituentsDefined());
//Getting for all configurations won't happen, because not all groups were set
rGroupQuery.GetAllConfigurations(); // Will raise exception
}
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);
}
public override void TestAcceptsAtLeastOneChemObjectClass()
{
RGroupQueryReader reader = new RGroupQueryReader(new StringReader(""));
Assert.IsTrue(reader.Accepts(typeof(RGroupQuery)));
}
public void TestRgroupQueryFile2()
{
var filename = "NCDK.Data.MDL.rgfile.2.mol";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new RGroupQueryReader(ins);
var rGroupQuery = (RGroupQuery)reader.Read(new RGroupQuery(ChemObjectBuilder.Instance));
reader.Close();
Assert.IsNotNull(rGroupQuery);
Assert.AreEqual(rGroupQuery.RGroupDefinitions.Count, 3);
Assert.AreEqual(rGroupQuery.RootStructure.Atoms.Count, 14);
Assert.AreEqual(rGroupQuery.RootAttachmentPoints.Count, 4);
var rGroupQueryAtoms = rGroupQuery.GetAllRgroupQueryAtoms();
Assert.AreEqual(rGroupQueryAtoms.Count, 4);
rGroupQueryAtoms = rGroupQuery.GetRgroupQueryAtoms(1);
Assert.AreEqual(rGroupQueryAtoms.Count, 1);
foreach (var at in rGroupQuery.GetAllRgroupQueryAtoms())
{
if (at is PseudoAtom)
{
Assert.IsTrue(RGroupQuery.IsValidRgroupQueryLabel(((PseudoAtom)at).Label));
var rgroupNum = int.Parse(((PseudoAtom)at).Label.Substring(1));
Assert.IsTrue(rgroupNum == 1 || rgroupNum == 2 || rgroupNum == 11);
switch (rgroupNum)
{
case 1:
{
//Test: R1 has two attachment points, defined by AAL
var rootApo = rGroupQuery.RootAttachmentPoints;
var apoBonds = rootApo[at];
Assert.AreEqual(apoBonds.Count, 2);
Assert.AreEqual(apoBonds[1].GetOther(at).Symbol, "N");
Assert.IsTrue(apoBonds[2].GetOther(at).Symbol.Equals("C"));
//Test: Oxygens are the 2nd APO's for R1
var rList = rGroupQuery.RGroupDefinitions[1];
Assert.AreEqual(rList.RGroups.Count, 2);
var rGroups = rList.RGroups;
Assert.AreEqual(rGroups[0].SecondAttachmentPoint.Symbol, "O");
Assert.AreEqual(rGroups[1].SecondAttachmentPoint.Symbol, "O");
Assert.IsFalse(rList.IsRestH);
}
break;
case 2:
{
RGroupList rList = rGroupQuery.RGroupDefinitions[2];
Assert.AreEqual(rList.RGroups.Count, 2);
Assert.AreEqual(rList.Occurrence, "0,2");
Assert.AreEqual(rList.RequiredRGroupNumber, 11);
Assert.IsFalse(rList.IsRestH);
}
break;
case 11:
{
RGroupList rList = rGroupQuery.RGroupDefinitions[11];
Assert.AreEqual(rList.RGroups.Count, 1);
Assert.AreEqual(rList.RequiredRGroupNumber, 0);
Assert.IsTrue(rList.IsRestH);
var rGroups = rList.RGroups;
Assert.AreEqual(rGroups[0].FirstAttachmentPoint.Symbol, "Pt");
Assert.AreEqual(rGroups[0].SecondAttachmentPoint, null);
}
break;
}
}
}
var configurations = rGroupQuery.GetAllConfigurations();
Assert.AreEqual(12, configurations.Count());
//Test restH values
int countRestHForSmallestConfigurations = 0;
foreach (var atc in configurations)
{
if (atc.Atoms.Count == 13)
{ // smallest configuration
foreach (var atom in atc.Atoms)
{
if (atom.GetProperty <bool?>(CDKPropertyName.RestH) != null)
{
countRestHForSmallestConfigurations++;
if (atom.Symbol.Equals("P"))
{
Assert.AreEqual(atom.GetProperty <bool>(CDKPropertyName.RestH), true);
}
}
}
}
}
Assert.AreEqual(countRestHForSmallestConfigurations, 6);
}