/// <summary>
/// NextRow - Return the next matching row value object
/// </summary>
/// <returns></returns>
public override Object[] NextRow()
{
throw new NotImplementedException();
#if false
string cid = "";
Molecule substituent = null;
Stopwatch swTotal = Stopwatch.StartNew();
Stopwatch sw = Stopwatch.StartNew();
if (Eqp.SearchKeySubset == null || Eqp.SearchKeySubset.Count == 0)
{
return(null);
}
// Get the structures for the set of keys
if (CidToStructureDict == null)
{
CidToStructureDict = MoleculeUtil.SelectMoleculesForCidList(Eqp.SearchKeySubset);
KeyListPos = -1;
MapPos = -1;
int msTime = (int)sw.ElapsedMilliseconds;
if (RGroupDecomp.Debug)
{
DebugLog.Message("Select " + Eqp.SearchKeySubset.Count + " structures time(ms): " + msTime);
}
}
// Get the next match
while (true)
{
if (KeyListPos < 0 || MapPos + 1 >= MapCount)
{ // go to next structure & set up mapping
KeyListPos++;
if (KeyListPos >= Eqp.SearchKeySubset.Count)
{
return(null);
}
cid = Eqp.SearchKeySubset[KeyListPos];
if (!CidToStructureDict.ContainsKey(cid))
{
continue;
}
MoleculeMx cs = CidToStructureDict[cid];
string molFile = cs.GetMolfileString();
//string chime = cs.ChimeString; // debug
if (RGroupDecomp.Debug)
{
DebugLog.StopwatchMessage("t1", sw);
}
if (DebugMx.False) // debug
{
//molFile = FileUtil.ReadFile(@"C:\Downloads\RGroupTarget.mol");
string targetSmiles = "CC1Cn2cc(c(= O)c3c2c(c(c(c3)F)Cl)S1)C(= O)O";
string targetChime = "CYAAFQwADfwQ19aXPcZERR45lQkn08$hZNXzeJ2yaAhDnxxJou4Gq9od8VG1ykiO63fQpvM8W4C6MR$O3VaZjQwrGr5weW3y^BeUEezndoIivvAbQN58EEHVMAsdPaF4LIsqsf$OCBUPHI5njBB2LIBy3i2cwbrD8T8kFVBVWkTCfIUFUtblI0G7vYiEL^svUWCT^m6tF18I7ISJUp^7WkuzpT9LrBSJLmMl5hHXog$68Q6YPb0^Xp0ftxmy7FDSF^sWib6^JrUMhrHtLfJ3yVMTm9RIrvvKMRQvKqq4G1Ooze5pdlpSdzp7MFl0K1zx4tdnNFoUO1kRPpyZks61qbBz2tU0L$svvojoU4yUlf$^MFF0nqSfGVW2PKv9TReb$knLXffdAAhqBN310WUfdJDoQBNX1a5L2uj9ybNNRLYpaZN1p6WYp2WI^ntQEVTBaJF1Uu28N4o2xudURpVITTKO7omUtpgLoaoOQHazmZG3k^aHPUOQfE0d27eAbE^uxcQUAB";
molFile = CdkMol.Util.MoleculeTofMolfileString(CdkMol.Util.ChimeStringToMolecule(targetChime));
}
Molecule target = CdkMol.Util.MolfileStringToMolecule(molFile);
if (RGroupDecomp.Debug)
{
DebugLog.StopwatchMessage("t2", sw);
}
MapCount = RGroupDecomp.ProcessTargetMolecule(target); // process & get number of maps
if (MapCount > 1)
{
MapCount = MapCount; // debug, seems to always be 1
}
MapPos = -1;
if (RGroupDecomp.Debug)
{
DebugLog.StopwatchMessage("t3", sw);
}
}
// Get the substituent for each RGroup for the next mapping
MapPos++; // get data for next mapping
for (int si = 0; si < Substituents.Length; si++) // clear substituents
{
Substituents[si] = null;
}
for (int fi = 0; fi < RgTotalCount; fi++)
{
Molecule fragment = RGroupDecomp.GetIthMappingFragment(MapPos, fi);
if (fragment == null)
{
break; // must have reached the end
}
if (RGroupDecomp.Debug)
{
DebugLog.StopwatchMessage("t4", sw);
}
int ri = CdkMol.Util.GetFragmentRGroupAssignment(fragment);
if (ri >= 0 && ri < Substituents.Length)
{
Substituents[ri] = fragment;
}
}
if (RGroupDecomp.Debug)
{
DebugLog.StopwatchMessage("t5", sw);
}
// Fill in the Vo
object[] vo = new object[Qt.SelectedCount];
for (int ci = 0; ci < SelectList.Count; ci++)
{
MetaColumn mc = SelectList[ci];
string name = mc.Name.ToLower();
if (mc.IsKey)
{
vo[ci] = Eqp.SearchKeySubset[KeyListPos];
}
else if (Lex.Eq(name, "Core"))
{
vo[ci] = CoreChemicalStructure;
}
else if (Lex.Eq(name, "Terminate_Option"))
{
vo[ci] = TerminateOptionString;
}
else if (Lex.Eq(name, "Map_Number"))
{
vo[ci] = (MapPos + 1).ToString();
}
else if (Lex.Eq(name, "Map"))
{
if (RGroupDecomp.Debug)
{
DebugLog.StopwatchMessage("t6", sw);
}
MoleculeMx cs = null;
try // hilight core molecule
{
if (StrMatcher == null) // initialize matcher with core structure if not done yet
{
StrMatcher = new StructureMatcher();
string molfile2 = CdkMol.Util.RemoveRGroupAttachmentPointAtoms(CoreChemicalStructure.GetMolfileString());
if (RGroupDecomp.Debug)
{
DebugLog.StopwatchMessage("t7", sw);
}
MoleculeMx cs2 = new MoleculeMx(MoleculeFormat.Molfile, molfile2);
StrMatcher.SetSSSQueryMolecule(cs2); // set core query used for highlighting
if (RGroupDecomp.Debug)
{
DebugLog.StopwatchMessage("t8", sw);
}
}
Molecule alignedTarget = RGroupDecomp.GetAlignedTargetForMapping(MapPos);
if (RGroupDecomp.Debug)
{
DebugLog.StopwatchMessage("t9", sw);
}
string chime = CdkMol.Util.MoleculeToChimeString(alignedTarget);
if (RGroupDecomp.Debug)
{
DebugLog.StopwatchMessage("t10", sw);
}
cs = new MoleculeMx(MoleculeFormat.Chime, chime);
cs = StrMatcher.HighlightMatchingSubstructure(cs);
}
catch (Exception ex) { ex = ex; }
vo[ci] = cs; // store value
if (RGroupDecomp.Debug)
{
DebugLog.StopwatchMessage("t11", sw);
}
}
else if (Lex.Eq(name, "Is_Map_Complete"))
{
vo[ci] = "Yes"; // always complete for PP
//else vo[ci] = "No";
}
else
{ // must be a substituent
if (RGroupDecomp.Debug)
{
DebugLog.StopwatchMessage("t12", sw);
}
int ri = name.IndexOf("_");
if (ri < 0 || !int.TryParse(name.Substring(1, ri - 1), out ri))
{
continue; // in case of bogus name
}
substituent = Substituents[ri];
if (substituent == null)
{
vo[ci] = null; // no mapping found
continue;
}
if (name.EndsWith("_structure"))
{
string chime = CdkMol.Util.MoleculeToChimeString(substituent);
MoleculeMx cs = new MoleculeMx(MoleculeFormat.Chime, chime);
vo[ci] = cs;
}
else if (name.EndsWith("_smiles"))
{
string smiles = CdkMol.Util.MoleculeToSmilesString(substituent);
vo[ci] = smiles;
}
else if (name.EndsWith("_formula"))
{
string mf = CdkMol.Util.GetMolFormulaDotDisconnect(substituent);
vo[ci] = mf;
}
else if (name.EndsWith("_weight"))
{
vo[ci] = CdkMol.Util.GetMolWeight(substituent);
}
else if (name.EndsWith("_substno"))
{
vo[ci] = ri;
}
if (RGroupDecomp.Debug)
{
DebugLog.StopwatchMessage("t13", sw);
}
}
}
int msTime = (int)sw.ElapsedMilliseconds;
if (RGroupDecomp.Debug)
{
DebugLog.StopwatchMessage("Total Time for Cid: " + cid, swTotal);
}
return(vo);
}
#endif
}
/// <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
}
