private void Timer_Tick(object sender, EventArgs e)
{
if (!StructureChanged)
{
return;
}
QueryColumn qc = ColInfo.Qc;
if (String.IsNullOrEmpty(StructureRenditor.MolfileString))
{
qc.SecondaryCriteria = qc.SecondaryCriteriaDisplay = "";
}
else
{
// Chime: CYAAFQwAncwQGj8h7GZ^yjgsajoFd0PQ1OYrnIdaPTl0lGnQYLHH2prJeJi$BhUHcMsE1TyQisJflsW2r293v92iC1^wVm$8wwLM7^krIFa8A1X6Jvu8VIYgCgJ8$y1RuqgCc5ifKbMAflB
string chimeString = MoleculeMx.MolfileStringToChimeString(StructureRenditor.MolfileString);
qc.SecondaryCriteria = "SSS ( " + qc.MetaColumn.Name + ", " + Lex.AddSingleQuotes(chimeString) + ") = 1";
qc.SecondaryCriteriaDisplay = qc.ActiveLabel + " contains substructure";
}
qc.SecondaryFilterType = FilterType.StructureSearch;
QueryManager.QueryResultsControl.UpdateFiltering(ColInfo);
FilterBasicCriteriaControl.SyncBaseQuerySecondaryCriteria(qc); // sync any base query
StructureChanged = false;
return;
}
private void StructureSearch_Click(object sender, EventArgs e)
{
QueryColumn qc = new QueryColumn();
MetaColumn mc = new MetaColumn(); // create minimal metacolumn with structure type to assoc with qc
mc.DataType = MetaColumnType.Structure;
qc.MetaColumn = mc;
bool gotCriteria = CriteriaStructure.Edit(qc);
if (!gotCriteria || qc.Criteria == "")
{
return;
}
string sid = "";
for (int si = 1; ; si++)
{
sid = "S" + si.ToString();
if (!LabeledCriteria.Structures.ContainsKey(sid.ToUpper()))
{
break;
}
}
string chime = MoleculeMx.MolfileStringToChimeString(qc.MolString); // get chime string
LabeledCriteria.Structures[sid.ToUpper()] = chime; // store sid & associated chime string
qc.MolString = chime;
string sCriteria = MqlUtil.ConvertQueryColumnStructureCriteriaToMql(qc);
sCriteria = sCriteria.Replace("(ctab,", "(structure_field,"); // required dummy field name
sCriteria = sCriteria.Replace(chime, "[Edit Structure " + sid + "]"); // substitute surrogate for structure
sCriteria = sCriteria.Replace("'[", "["); // hack fixup
sCriteria = sCriteria.Replace("]'", "]");
Instance.InsertCriteria(sCriteria);
}
/// <summary>
/// Initialize for any structure hilighting
/// </summary>
void InitializeStructureHilighting()
{
QueryColumn qc = null;
if (StructureHighlightingInitialized)
{
return;
}
// Structure match hilighting / orienting
try
{
do
{
qc = Query.GetFirstStructureCriteriaColumn();
if (qc == null)
{
break;
}
if (Lex.IsUndefined(qc.Criteria))
{
break;
}
ParsedSingleCriteria psc = MqlUtil.ParseQueryColumnCriteria(qc);
if (psc == null || Lex.IsUndefined(psc.Value))
{
break;
}
ParsedStructureCriteria pssc = ParsedStructureCriteria.ConvertFromPscToPssc(psc);
StructureDisplayFormat sdf = StructureDisplayFormat.Deserialize(qc.DisplayFormatString); // get any hilighting info from format
if (pssc.SearchType == StructureSearchType.Substructure)
{
string chime = MoleculeMx.MolfileStringToChimeString(qc.MolString);
if (!String.IsNullOrEmpty(chime))
{
AlignStructureToQuery = Lex.Contains(psc.Value2, "Orient") || Lex.Contains(psc.Value2, "Align=True");
HighlightStructureMatches = !(Lex.Contains(psc.Value2, "NoHighlight") || Lex.Contains(psc.Value2, "Highlight=false"));
MoleculeMx cs = new MoleculeMx(MoleculeFormat.Chime, chime);
StrMatcher = new StructureMatcher();
StrMatcher.SetSSSQueryMolecule(cs); // set query used for highlighting
}
}
else if (pssc.SearchType == StructureSearchType.SmallWorld && pssc.SmallWorldParameters != null)
{
SmallWorldPredefinedParameters swp = pssc.SmallWorldParameters;
HighlightStructureMatches = swp.Highlight;
AlignStructureToQuery = swp.Align;
//SmallWorldDepictions = null; // depiction cache
}
else if (pssc.SearchType == StructureSearchType.Related) //
{
string chime = MoleculeMx.MolfileStringToChimeString(qc.MolString);
if (!String.IsNullOrEmpty(chime))
{
AlignStructureToQuery = Lex.Contains(psc.Value2, "Orient") || Lex.Contains(psc.Value2, "Align=True");
HighlightStructureMatches = !(Lex.Contains(psc.Value2, "NoHighlight") || Lex.Contains(psc.Value2, "Highlight=false"));
MoleculeMx cs = new MoleculeMx(MoleculeFormat.Chime, chime);
StrMatcher = new StructureMatcher();
StrMatcher.SetSSSQueryMolecule(cs); // set query used for SSS highlighting
}
}
else if (sdf.Highlight || sdf.Align) // other cases
{
HighlightStructureMatches = sdf.Highlight;
AlignStructureToQuery = sdf.Align;
}
else
{
break; // no hilighting / orienting
}
StructureHighlightQc = qc;
StructureHighlightPssc = pssc;
} while (false);
}
catch (Exception ex) // log & ignore any errors
{
string msg = DebugLog.FormatExceptionMessage(ex);
if (qc != null)
{
msg += "\r\n" +
"Criteria: " + qc.Criteria + "\r\n" +
"Molstring: " + qc.MolString;
}
DebugLog.Message(msg);
return;
}
// Atom number display (not currently used)
SS.I.DisplayAtomNumbers = (int)AtomNumberDisplayMode.None; // see if need to display atom numbers
for (int ti = 1; ti < Rf.Tables.Count; ti++)
{
ResultsTable rt = Rf.Tables[ti];
MetaTable mt = rt.MetaTable;
if (mt.Name.IndexOf("todo: table that needs atom number display") >= 0)
{
SS.I.DisplayAtomNumbers = (int)AtomNumberDisplayMode.All;
break;
}
}
StructureHighlightingInitialized = true;
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
}