/// <summary>
/// SetupQueryTableForRGroupDecomposition
/// </summary>
/// <param name="qt"></param>
/// <param name="q"></param>
public void SetupQueryTableForRGroupDecomposition(
QueryTable qt,
Query q)
{
Stopwatch sw = Stopwatch.StartNew();
MetaTable mt = qt.MetaTable;
QueryColumn qc = qt.GetQueryColumnByName("core");
if (qc == null)
{
throw new UserQueryException("Core column not defined in rgroup_decomposition table");
}
string molfile = qc.MolString;
if (molfile == null || molfile == "")
{ // core not defined in Rgroup decomposition table, try to get from structure search in rest of query
foreach (QueryTable qt3 in q.Tables)
{
if (!qt3.MetaTable.IsRootTable)
{
continue;
}
MetaColumn mc3 = qt3.MetaTable.FirstStructureMetaColumn;
if (mc3 != null)
{
QueryColumn qc3 = qt3.GetQueryColumnByName(mc3.Name);
molfile = qc3.MolString;
break;
}
}
}
if (molfile == null || molfile == "")
{
throw new UserQueryException("R-group decomposition core structure is not defined");
}
MoleculeMx cs = new MoleculeMx(MoleculeFormat.Molfile, molfile);
cs.GetCoreRGroupInfo(out RgCounts, out RgTotalCount);
if (RgCounts.Count == 0 || (RgCounts.ContainsKey(0) && RgCounts.Count == 1))
{
throw new UserQueryException("R-group decomposition core structure must contain at least one numbered R-group");
}
qc = qt.GetQueryColumnByName("R1_Structure"); // update any core structure label
if (qc == null)
{
throw new UserQueryException("Can't find R1_Structure in " + mt.Label);
}
if (qc.Label.IndexOf("\tChime=") > 0)
{
qc.Label = "R-group, Core\tChime=" + cs.GetChimeString(); // reference core in query col header label
qc.MetaColumn.Width = 25;
}
SetRnToMatchR1(qt, "Structure"); // reset querycolumn selection & width to match R1
SetRnToMatchR1(qt, "Smiles");
SetRnToMatchR1(qt, "Formula");
SetRnToMatchR1(qt, "Weight");
SetRnToMatchR1(qt, "SubstNo");
int msTime = (int)sw.ElapsedMilliseconds;
//if (RGroupDecomp.Debug) DebugLog.Message("Time(ms): " + msTime);
return;
}
/// <summary>
/// Do setup in preparation for decompose
/// </summary>
/// <param name="qt"></param>
/// <param name="q"></param>
public void PrepareForDecompose(
QueryTable qt,
Query q)
{
throw new NotImplementedException();
#if false
Stopwatch sw = Stopwatch.StartNew();
MetaTable mt = qt.MetaTable;
QueryColumn qc = qt.GetQueryColumnByName("core");
if (qc == null)
{
throw new UserQueryException("Core column not defined in rgroup_decomposition table");
}
string molfile = qc.MolString;
if (molfile == null || molfile == "")
{ // core not defined in Rgroup decomposition table, try to get from structure search in rest of query
foreach (QueryTable qt3 in q.Tables)
{
if (!qt3.MetaTable.IsRootTable)
{
continue;
}
MetaColumn mc3 = qt3.MetaTable.FirstStructureMetaColumn;
if (mc3 != null)
{
QueryColumn qc3 = qt3.GetQueryColumnByName(mc3.Name);
molfile = qc3.MolString;
break;
}
}
}
if (molfile == null || molfile == "")
{
throw new UserQueryException("R-group decomposition core structure is not defined");
}
bool allowHydrogenSubstituents = true;
qc = qt.GetQueryColumnByName("AllowHydrogenSubstituents");
if (Lex.Contains(qc?.Criteria, "'N'"))
{
allowHydrogenSubstituents = false; // set to false if "no" criteria specified
}
TerminateOptionString = "First mapping";
bool allowMultipleCoreMappings = false;
qc = qt.GetQueryColumnByName("Terminate_Option");
if (qc != null && qc.Criteria != "")
{
ParsedSingleCriteria psc = MqlUtil.ParseSingleCriteria(qc.Criteria);
TerminateOptionString = psc.Value;
allowMultipleCoreMappings = Lex.Contains(TerminateOptionString, "All");
}
MoleculeMx cs = new MoleculeMx(MoleculeFormat.Molfile, molfile);
cs.GetCoreRGroupInfo(out RgCounts, out RgTotalCount); // need to redefine these
RGroupDecomp.Initialize();
RGroupDecomp.SetAlignStructuresToCore(true);
RGroupDecomp.SetAllowMultipleCoreMappings(allowMultipleCoreMappings);
RGroupDecomp.SetIncludeHydrogenFragments(allowHydrogenSubstituents);
if (DebugMx.True) // debug
{
String coreSmiles = "[R1]c1cn2c3c(c1= O)cc(c(c3SC(C2)[R4])[R3])[R2]";
string coreChime = "CYAAFQwAUewQeV58YHemfM^EQqPRfIYlJGEkx6M7e4db95jjK5HrNFVP2e1qHphWPL98KvcvrsF7bP9bRcW4QH$si9PXkkuwre6Q5UkHZjciQqeAKVLSHNAeQTAMlkiXEBD$BePpbNQCPD3BkklFEaQqwokeI$FwUoS5cAixQXkMbLTWDaAK7t7cOkSmt3RhwQedbrba6OHKBq3OF4Dhlz$0BfLeKCUUo8ixle176M2aIzXUccTOU8Xy8ARwE3bTyMfjuI3UunZceJf4iZELvsj3PX2MHZG73baUvQGS4DaxUaBGps81PPiDljfvxwFv8OfdOyIRlOBeuEAvk2rT9SRT6oMZIV6UtLFvmCHdwKnu9WtrfV1rEctydNUVxW4qKVlV0rZtpK1oZXuKcv6WVdl6r2hrjVLxBhblTVKO7w1qGRoziquOnPQkKd9H4EQfV0rP6mzI8Au8ulti2fu3YKB94lPXftPGbwr5yA";
IMolLib coreMol = MolLibFactory.NewMolLib(MoleculeFormat.Molfile, molfile);
coreChime = MoleculeMx.MolfileStringToChimeString(molfile);
molfile = coreMol.MolfileString;
}
CoreMolecule = CdkMol.Util.MolfileStringToMolecule(molfile);
RGroupDecomp.SetCoreStructure(CoreMolecule, false);
CoreChemicalStructure = new MoleculeMx(MoleculeFormat.Molfile, molfile);
StrMatcher = null;
int msTime = (int)sw.ElapsedMilliseconds;
if (RGroupDecomp.Debug)
{
DebugLog.Message("Time(ms): " + msTime);
}
return;
#endif
}