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 }