/// <summary>
/// Get related compound ids & update display
/// </summary>
/// <param name="parm"></param>
void SearchAndRetrieveRelatedStructuresThreadMethod(object parm)
{
try
{
int searchId = 0; // id for search associated with this thread
lock (RSMLock)
{
SearchCounter++; // assign id for the search associated with this thread
searchId = SearchCounter;
}
RelatedStructureSearchResults rss = RelatedStructureSearchResults.SearchHistory(Cid, CidMtName);
if (rss == null || Lex.IsUndefined(Cid) || Lex.IsUndefined(CidMtName) || !UseCachedResults)
{
PendingStatusMessage = "Searching...";
rss = new RelatedStructureSearchResults();
rss.Cid = Cid;
rss.CidMtName = CidMtName;
if (Debug)
{
DebugLog.Message("=== Client === " + searchId + ". Starting search for CID: " + Cid + " =========");
}
string hitString = MoleculeUtil.GetRelatedMatchCounts(Cid, CidMtName, QueryStruct.GetChimeString(), SearchTypes, searchId);
if (Superseded(searchId))
{
return; // return now if superceded and no longer needed
}
if (Debug)
{
DebugLog.Message("=== Client === " + searchId + ". Search step complete: " + hitString);
}
if (Lex.IsUndefined(hitString))
{
if (Debug)
{
DebugLog.Message("=== Client === " + searchId + ". Hit string is undefined.");
}
return;
}
string[] sa = hitString.Split(';');
if (sa.Length != 10)
{
return;
}
rss.AltCorpDbCnt = int.Parse(sa[0]);
rss.SimCorpDbCnt = int.Parse(sa[1]);
rss.MmpCorpDbCnt = int.Parse(sa[2]);
rss.SwCorpDbCnt = int.Parse(sa[3]);
rss.CorpDbCnt = int.Parse(sa[4]);
rss.AltChemblCnt = int.Parse(sa[5]);
rss.SimChemblCnt = int.Parse(sa[6]);
rss.MmpChemblCnt = int.Parse(sa[7]);
rss.SwChemblCnt = int.Parse(sa[8]);
rss.ChemblCnt = int.Parse(sa[9]);
RelatedStructureSearchResults.History.Add(rss);
}
RelatedStructuresResults = rss;
RenderResultsRequested = true; // request render of initial results
if (rss.CorpDbCnt <= 0 && rss.ChemblCnt <= 0) // if no hits then assign empty structure list and don't do retrieve
{
rss.MatchList = new List <StructSearchMatch>();
}
if (rss.MatchList == null) // retrieve structures if structure list doesn't exist
{
if (Debug)
{
DebugLog.Message("=== Client === " + searchId + ". Starting structure retrieval...");
}
PendingStatusMessage = "Retrieving...";
rss.Cid = Cid;
rss.CidMtName = CidMtName;
List <StructSearchMatch> ssml = MoleculeUtil.GetRelatedMatchRows(Cid, CidMtName);
if (Superseded(searchId))
{
return; // return now if superceded and no longer needed
}
rss.MatchList = ssml;
if (Debug)
{
DebugLog.Message("=== Client === " + searchId + ". Structure retrieval complete");
}
}
else
{
if (Debug)
{
DebugLog.Message("=== Client === " + searchId + ". Already have structures");
}
}
PendingStatusMessage = "";
RenderResultsRequested = true; // request render of associated structures
StructureRetrievalCompletedRenderRequest = true;
if (Debug)
{
DebugLog.Message("=== Client === " + searchId + ". Search and retrieval complete");
}
return;
}
catch (Exception ex) // log any exception since any thrown exception for thread can't be caught
{
DebugLog.Message(ex);
}
}
/// <summary>
/// Build query table for decomposition & add to query
/// </summary>
/// <returns></returns>
DialogResult ProcessInput()
{
Query q;
MetaTable mt;
MetaColumn mc;
QueryTable qt;
QueryColumn qc;
q = QbUtil.Query;
if (q == null || q.Tables.Count == 0)
{
MessageBoxMx.ShowError("No current query.");
return(DialogResult.None);
}
qt = q.GetQueryTableByName("Rgroup_Decomposition");
bool newTable = false;
if (qt == null)
{
mt = MetaTableCollection.GetWithException("Rgroup_Decomposition");
qt = new QueryTable(mt);
newTable = true;
}
qc = qt.GetQueryColumnByNameWithException("Core");
MoleculeMx core = new MoleculeMx(MoleculeFormat.Molfile, QueryMolCtl.MolfileString);
if (core.AtomCount == 0)
{
MessageBoxMx.ShowError("A Core structure with R-groups must be defined.");
return(DialogResult.None);
}
qc.MolString = core.GetMolfileString(); // put core structure into table criteria
qc.CriteriaDisplay = "Substructure search (SSS)";
qc.Criteria = "CORE SSS SQUERY";
if (!Structure.Checked && !Smiles.Checked && !Formula.Checked &&
!Weight.Checked && !Index.Checked)
{
MessageBoxMx.ShowError("At least one substituent display format must be selected.");
return(DialogResult.None);
}
qc = qt.GetQueryColumnByName("R1_Structure");
if (ShowCoreStructure.Checked)
{
qc.Label = "R-group, Core\tChime=" + core.GetChimeString(); // reference core in query col header label
qc.MetaColumn.Width = 25;
}
SetSelected(qt, "R1_Structure", Structure.Checked);
SetSelected(qt, "R1_Smiles", Smiles.Checked);
SetSelected(qt, "R1_Formula", Formula.Checked);
SetSelected(qt, "R1_Weight", Weight.Checked);
SetSelected(qt, "R1_SubstNo", Index.Checked);
string terminateOption = TerminateOption.Text;
qc = qt.GetQueryColumnByName("Terminate_Option");
if (qc != null && Lex.IsDefined(terminateOption))
{
qc.Criteria = qt.MetaTable.Name + " = " + Lex.AddSingleQuotes(terminateOption);
qc.CriteriaDisplay = "= " + Lex.AddSingleQuotes(terminateOption);
}
else
{
qc.Criteria = qc.CriteriaDisplay = ""; // not defined
}
if (newTable)
{
q.AddQueryTable(qt); // add to query if new
}
QbUtil.RenderQuery(); // show it
UsageDao.LogEvent("RgroupDecomposition");
return(DialogResult.OK);
}
/// <summary>
/// Search button clicked, process input
/// </summary>
/// <returns></returns>
DialogResult ProcessInput()
{
CidList cidList = null;
StreamReader structureFileReader = null;
string qid; // query identifier, compoundId, file name or sdFile key value
QueryManager qm;
DataTableMx dt;
DataColumn dc;
DataRowMx dr;
//object[] dr; // if using Qe
DialogResult dlgRslt = DialogResult.OK;
Query q = null;
QueryTable qt = null;
QueryColumn simScoreQc, structQc; // query column containing latest query settings
MetaTable mt = null;
MetaColumn keyMc = null, structMc = null, dbSetMc = null, simScoreMc = null, mc;
MetaColumnType storageType;
string txt, tok;
if (DatabasesToSearch.Text == "")
{
MessageBoxMx.ShowError("Databases to search must be defined.");
DatabasesToSearch.Focus();
return(DialogResult.Cancel);
}
// Get list of databases
string[] dba = DatabasesToSearch.Text.Split(',');
List <MetaTable> tables = new List <MetaTable>();
foreach (string dbLabel0 in dba)
{
string dbLabel = dbLabel0.Trim();
RootTable dbInfo = RootTable.GetFromTableLabel(dbLabel);
if (dbInfo == null)
{
MessageBoxMx.ShowError("Can't find database " + DatabasesToSearch.Text);
DatabasesToSearch.Focus();
return(DialogResult.Cancel);
}
mt = MetaTableCollection.Get(dbInfo.MetaTableName);
if (mt == null)
{
MessageBoxMx.ShowError("Unable to locate parent structure table for database: " + DatabasesToSearch.Text);
DatabasesToSearch.Focus();
return(DialogResult.Cancel);
}
if (dbSetMc == null)
{
dbSetMc = mt.DatabaseListMetaColumn;
}
tables.Add(mt);
}
if (dbSetMc == null)
{
throw new Exception("\"Databases\" metacolumn not found for any of the databases to search");
}
// Validate other form values
RetrieveStructures = RetrieveMatchingStructures.Checked;
bool fromList = FromList.Checked;
int listCidsRead = 0;
int inputQueryCount = -1;
if (fromList) // using list, validate list name
{
if (SavedListUo == null)
{
MessageBoxMx.ShowError("Compound list must be defined.");
ListName.Focus();
return(DialogResult.Cancel);
}
cidList = CidListCommand.Read(SavedListUo);
if (cidList == null)
{
MessageBoxMx.ShowError("Error reading list.");
ListName.Focus();
return(DialogResult.Cancel);
}
inputQueryCount = cidList.Count;
}
else // Using SdFile, validate SdFile name
{
StructureFile = FileName.Text;
if (StructureFile == "")
{
MessageBoxMx.ShowError("File must be defined.");
FileName.Focus();
return(DialogResult.Cancel);
}
try { structureFileReader = new StreamReader(StructureFile); structureFileReader.Close(); }
catch (Exception ex)
{
MessageBoxMx.ShowError("Can't read file: " + Lex.Dq(StructureFile));
FileName.Focus();
return(DialogResult.Cancel);
}
keyField = KeyField.Text; // get key, blank to use name in 1st line
inputQueryCount = -1; // don't know how many queries unless we read the file (todo?)
}
tok = ResultsName.Text.Trim(); // name to store results under
if (tok == "")
{
MessageBoxMx.ShowError("A name for the results must be provided.");
ResultsName.Focus();
return(DialogResult.Cancel);
}
if (SubStruct.Checked)
{
Psc.SearchType = StructureSearchType.Substructure;
}
else if (Full.Checked)
{
Psc.SearchType = StructureSearchType.FullStructure;
}
else if (Similarity.Checked)
{
Psc.SearchType = StructureSearchType.MolSim;
}
else
{
throw new Exception("Unrecognized search type");
}
// Write initial log entries
SearchCount++;
string logFileName = ClientDirs.DefaultMobiusUserDocumentsFolder + @"\Multistructure Search " + SearchCount + ".txt";
if (!UIMisc.CanWriteFileToDefaultDir(logFileName))
{
return(DialogResult.Cancel);
}
LogStream = new StreamWriter(logFileName);
if (ResultsUo == null)
{
ResultsUo = new UserObject(UserObjectType.Annotation);
}
ResultsUo.Name = tok;
UserObjectTree.GetValidUserObjectTypeFolder(ResultsUo);
DateTime startTime = DateTime.Now;
WriteToLog("Multiple " + Psc.SearchType + " Search");
WriteToLog("Databases: " + DatabasesToSearch.Text);
WriteToLog("Date: " + startTime);
if (fromList)
{
WriteToLog("Input List: " + SavedListUo.Name);
}
else
{
WriteToLog("Input Structure File: " + StructureFile);
}
WriteToLog("Output List: " + ResultsUo.Name);
WriteToLog("Log File: " + logFileName);
WriteToLog("");
WriteToLog("Query, Match, Score");
int queryCount = 0;
int matchAtLeastOneCount = 0;
MoleculeMx queryStructure = null; // current structure being searched
CidList matchList = new CidList();
List <MatchData> matchData = new List <MatchData>();
if (FromFile.Checked) // open SdFile as required
{
structureFileReader = new StreamReader(StructureFile);
}
// Search of structures one at a time
while (true)
{
if (fromList) // get next structure from list
{
if (listCidsRead >= cidList.Count)
{
break;
}
qid = cidList[listCidsRead].Cid;
listCidsRead++;
if (qid.Trim() == "")
{
continue;
}
if (qid.ToLower().IndexOf(".mol") > 0 || qid.ToLower().IndexOf(".skc") > 0)
{ // file reference
if (!File.Exists(qid))
{
continue;
}
if (qid.ToLower().IndexOf(".mol") > 0)
{
queryStructure = MoleculeMx.ReadMolfile(qid);
}
else
{
queryStructure = MoleculeMx.ReadSketchFile(qid);
}
}
else
{
queryStructure = MoleculeUtil.SelectMoleculeForCid(qid);
}
if (queryStructure == null || queryStructure.AtomCount == 0)
{
continue; // oops
}
}
else // get next structure from input file
{
qid = null;
if (StructureFile.ToLower().EndsWith(".sdf"))
{
List <SdFileField> fList = SdFileDao.Read(structureFileReader);
if (fList == null) // end of sdFile
{
structureFileReader.Close();
break;
}
if (fList.Count == 0)
{
continue;
}
queryStructure = new MoleculeMx(MoleculeFormat.Molfile, fList[0].Data);
if (queryStructure == null || queryStructure.AtomCount == 0)
{
continue;
}
if (keyField != "") // key field specified?
{
qid = SdFileDao.GetDataField(fList, keyField);
}
else // get name from 1st line of molfile
{
string molFile = fList[0].Data;
int i1 = molFile.IndexOf("\n");
if (i1 == 0)
{
qid = "";
}
else
{
qid = molFile.Substring(0, i1).Trim();
}
}
if (string.IsNullOrEmpty(qid))
{
qid = SdFileDao.GetDataField(fList, "compound_id");
}
}
else // assume smiles file
{
string smiles = structureFileReader.ReadLine();
if (smiles == null) // end of sdFile
{
structureFileReader.Close();
break;
}
smiles = smiles.Trim();
if (smiles.Length == 0)
{
continue;
}
int i1 = smiles.IndexOf(","); // get any preceeding queryId
if (i1 < 0)
{
i1 = smiles.IndexOf("\t");
}
if (i1 >= 0)
{
qid = smiles.Substring(0, i1).Trim();
smiles = smiles.Substring(i1 + 1).Trim();
}
queryStructure = new MoleculeMx(MoleculeFormat.Smiles, smiles);
if (queryStructure == null || queryStructure.AtomCount == 0)
{
continue;
}
}
if (qid == null || qid.Trim() == "")
{
qid = (queryCount + 1).ToString(); // be sure we have a query id
}
}
queryCount++; // count the query
if (queryStructure == null || queryStructure.AtomCount == 0)
{
WriteToLog("Error converting specific structure " + queryCount.ToString() + ", " + qid);
continue;
}
queryStructure.RemoveStructureCaption(); // remove any Mobius-added caption
Psc.Molecule = queryStructure;
string msg =
"Searching Structure: " + queryCount.ToString();
if (inputQueryCount > 0)
{
msg += " of " + inputQueryCount.ToString();
}
msg += "\n" +
"Structures with one or more matches: " + matchAtLeastOneCount.ToString() + "\n" +
"Total Matches: " + matchList.Count.ToString();
Progress.Show(msg);
// Do the search over the list of databases
for (int ti = 0; ti < tables.Count; ti++)
{
mt = tables[ti];
q = new Query(); // build basic query
//q.SingleStepExecution = true; // do in single step (doesn't currently return sim score)
q.ShowStereoComments = false;
qt = new QueryTable(mt);
q.AddQueryTable(qt);
qt.SelectKeyOnly(); // start selecting desired cols
keyMc = mt.KeyMetaColumn;
structMc = mt.FirstStructureMetaColumn;
structQc = qt.GetQueryColumnByName(structMc.Name);
structQc.Selected = RetrieveStructures;
dbSetMc = mt.DatabaseListMetaColumn;
if (dbSetMc == null)
{
throw new Exception("\"Databases\" metacolumn not found for table: " + mt.Label);
}
QueryColumn dbSetQc = qt.GetQueryColumnByName(dbSetMc.Name);
dbSetQc.Selected = true; // select the database name
RootTable root = RootTable.GetFromTableName(mt.Name);
txt = " in (" + root.Label + ")";
dbSetQc.Criteria = dbSetMc.Name + txt;
dbSetQc.CriteriaDisplay = txt;
simScoreMc = mt.SimilarityScoreMetaColumn;
simScoreQc = null;
if (simScoreMc != null) // get sim score if it exists
{
simScoreQc = qt.GetQueryColumnByName(simScoreMc.Name);
simScoreQc.Selected = true; // return sim score
}
Psc.QueryColumn = structQc;
ParsedStructureCriteria psc2 = AdjustSearchForSmallWorldAsNeeded(Psc);
psc2.ConvertToQueryColumnCriteria(structQc); // format the QC for the structure search
DateTime t0 = DateTime.Now;
//QueryEngine qe = new QueryEngine();
//qe.NextRowsMin = 1000; // minimum number of rows to prefetch
//qe.NextRowsMax = -1; // maximum number of rows to prefetch
//qe.NextRowsMaxTime = 10000; // max time in milliseconds for next fetch
//qe.ExecuteQuery(q);
qm = new QueryManager();
try { dlgRslt = qm.ExecuteQuery(ref q); }
catch (Exception ex)
{
WriteToLog("Error searching structure: " + ex.Message + ", " + queryCount.ToString() + ", " + qid);
continue;
}
if (dlgRslt != DialogResult.OK)
{
return(dlgRslt);
}
double executeTime = TimeOfDay.Delta(ref t0);
int offset = qm.DataTableManager.KeyValueVoPos + 1;
//int offset = 0; // for QE
int keyPos = offset++;
int strPos = RetrieveStructures ? offset++ : -1;
int dbPos = offset++;
int simPos = offset++;
int fetchCnt = 0;
while (true)
{
dr = qm.NextRow();
//dr = qe.NextRow(); // for Qe
if (dr == null)
{
break;
}
fetchCnt++;
if (fetchCnt == 1)
{
matchAtLeastOneCount++; // number of queries that have at least one match
}
MatchData md = new MatchData();
md.Qno = queryCount;
md.Qid = qid;
if (RetrieveStructures)
{
md.Qstr = "Chime=" + queryStructure.GetChimeString();
}
CompoundId cid = CompoundId.ConvertTo(dr[keyPos]);
md.Mid = cid.Value;
if (RetrieveStructures)
{
MoleculeMx ms = MoleculeMx.ConvertTo(dr[strPos]);
if (!NullValue.IsNull(ms))
{
md.Mstr = "Chime=" + ms.GetChimeString();
}
}
StringMx db = StringMx.ConvertTo(dr[dbPos]);
if (!NullValue.IsNull(db))
{
md.Db = db.Value;
}
if (Psc.SearchType == StructureSearchType.MolSim)
{
NumberMx nex = NumberMx.ConvertTo(dr[simPos]);
if (!NullValue.IsNull(nex))
{
md.Score = nex.Value;
}
}
if (matchList.Contains(cid.Value)) // already have compound id as match for other query?
{
if (Psc.SearchType != StructureSearchType.MolSim)
{
continue; // if similarity search see if more similar
}
CidListElement le = matchList.Get(cid.Value); // reference current score
if (le.Tag > md.Score)
{
continue; // only replace if more similar
}
matchList.Remove(le.Cid); // remove from list
for (int mi = 0; mi < matchData.Count; mi++) // remove from data
{
if (matchData[mi].Mid == md.Mid)
{
matchData.RemoveAt(mi);
break;
}
}
}
matchList.Add(md.Mid);
matchList.Get(md.Mid).Tag = md.Score; // keep score in list
matchData.Add(md); // add to results
txt = md.Qid + ", " + md.Mid + ", " + md.Score.ToString();
WriteToLog(txt);
} // Fetch result loop
double fetchTime = TimeOfDay.Delta(ref t0);
} // DB loop
if (Progress.CancelRequested)
{
Progress.Hide();
MessageBoxMx.ShowError("Search cancelled.");
try { LogStream.Close(); } catch { }
return(DialogResult.Cancel);
}
} // key loop
CidListCommand.WriteCurrentList(matchList); // write the list of numbers
UsageDao.LogEvent("MultipleStructSearch");
txt =
"=== Multiple structure search complete ===\r\n\r\n" +
"Structures Searched: " + queryCount.ToString() + "\r\n";
txt +=
"Structures with one or more matches: " + matchAtLeastOneCount.ToString() + "\r\n" +
"Total Matches: " + matchList.Count.ToString() + "\r\n";
TimeSpan ts = DateTime.Now.Subtract(startTime);
ts = new TimeSpan(ts.Hours, ts.Minutes, ts.Seconds);
txt += "Total Time: " + ts + "\r\n\r\n";
WriteToLog("\r\n" + txt);
try { LogStream.Close(); } catch { }
if (matchList.Count == 0)
{
Progress.Hide();
MessageBoxMx.ShowError("No matches have been found.");
return(DialogResult.Cancel);
}
tok = "Matching compound ids";
if (Psc.SearchType == StructureSearchType.MolSim)
{
tok = "Similar compound ids";
}
txt += tok + " have been written to the current list: " + ResultsUo.Name + "\n" +
"Log file written to: " + logFileName + "\n\n" +
"Do you want to view the match results?";
DialogResult dRslt = MessageBoxMx.Show(txt, "Multiple Structure Search", MessageBoxButtons.YesNoCancel, MessageBoxIcon.Question);
if (dRslt == DialogResult.Cancel)
{
return(DialogResult.Cancel);
}
else if (dRslt == DialogResult.No) // show log
{
SystemUtil.StartProcess(logFileName);
return(DialogResult.Cancel);
}
// Display results
Progress.Show("Formatting results...");
mt = new MetaTable();
mt.Name = "MULTSTRUCTSEARCH_" + SearchCount;
mt.Label = "Multiple Structure Search " + SearchCount;
mt.TableMap = "Mobius.Tools.MultStructSearch"; // plugin id
mt.MetaBrokerType = MetaBrokerType.NoSql;
ColumnSelectionEnum structureColumnSelection = RetrieveStructures ? ColumnSelectionEnum.Selected : ColumnSelectionEnum.Unselected;
keyMc = keyMc.Clone();
keyMc.Name = "MatchingCid";
keyMc.Label = "Matching Compound Id";
mt.AddMetaColumn(keyMc);
structMc = structMc.Clone();
structMc.Name = "MatchingStructure";
structMc.Label = "Matching Structure";
structMc.InitialSelection = structureColumnSelection;
mt.AddMetaColumn(structMc);
dbSetMc = dbSetMc.Clone();
dbSetMc.Name = "Database";
mt.AddMetaColumn(dbSetMc);
//if (DatabasesToSearch.Text.Contains(","))
dbSetMc.InitialSelection = ColumnSelectionEnum.Selected;
mc = mt.AddMetaColumn("Molsimilarity", "Similarity Search Score", MetaColumnType.Number, ColumnSelectionEnum.Unselected, 10);
if (Psc.SearchType == StructureSearchType.MolSim)
{
mc.InitialSelection = ColumnSelectionEnum.Selected;
}
mc = mt.AddMetaColumn("QueryNo", "Query Number", MetaColumnType.Integer);
//mc = mt.AddMetaColumn("QueryMatchNo", "Query Match Number", MetaColumnType.Integer);
mc = mt.AddMetaColumn("QueryId", "Query Id", MetaColumnType.String);
mc = mt.AddMetaColumn("QueryStructure", "Query Structure", MetaColumnType.Structure);
mc.InitialSelection = structureColumnSelection;
q = ToolHelper.InitEmbeddedDataToolQuery(mt);
dt = q.ResultsDataTable as DataTableMx;
for (int mi = 0; mi < matchData.Count; mi++)
{
MatchData md = matchData[mi];
dr = dt.NewRow();
dr[qt.Alias + ".MatchingCid"] = new CompoundId(md.Mid);
if (RetrieveStructures)
{
dr[qt.Alias + ".MatchingStructure"] = new MoleculeMx(MoleculeFormat.Chime, md.Mstr);
}
dr[qt.Alias + ".Database"] = new StringMx(md.Db);
if (Psc.SearchType == StructureSearchType.MolSim)
{
dr[qt.Alias + ".Molsimilarity"] = new NumberMx(md.Score);
}
dr[qt.Alias + ".QueryNo"] = new NumberMx(md.Qno);
dr[qt.Alias + ".QueryId"] = new StringMx(md.Qid);
if (RetrieveStructures)
{
dr[qt.Alias + ".QueryStructure"] = new MoleculeMx(MoleculeFormat.Chime, md.Qstr);
}
dt.Rows.Add(dr);
}
ToolHelper.DisplayData(q, dt, true);
Progress.Hide();
return(DialogResult.OK);
}
/// <summary>
/// Format a chemical structure for Html output
/// </summary>
/// <param name="mol"></param>
/// <param name="destRect"></param>
/// <param name="width"></param>
/// <param name="r"></param>
/// <returns></returns>
string FormatChemStructureHtml(
MoleculeMx mol,
Rectangle destRect,
int width,
int r)
{
string source, molfil, html, shtml, fname, txt, txt2, str, hdisp, rntxt, html_end;
int width2, pixWidth, pixHeight, height, rc, i1;
bool useChimeString = false; // must use molfile format for .Net 4.0 with Draw 4.0
MolCount++;
string objId = "Mol" + MolCount;
//double scaleUp = (SS.I.GraphicsColumnZoom / 100.0) * 1.2; // do graphics scaleup plus a bit
double scaleUp = 1.2; // extra scaleup
pixWidth = (int)(width / 1000.0 * GraphicsMx.LogicalPixelsX * scaleUp);
height = (int)(width * .67);
if (destRect.Height > height)
{
height = destRect.Height;
}
pixHeight = (int)(height / 1000.0 * GraphicsMx.LogicalPixelsY * scaleUp);
shtml = // html for structure
"<object id=\"" + objId + "\" " +
"codebase=\"<editor>.dll#-1,-1,-1,-1\" " +
"height=\"<pixHeight>\" width=\"<pixWidth>\" " +
"classid=\"CLSID:46803AAE-C327-4002-8CEC-05036E2FDEF4\"> " + //
"<param name=\"<molStringFormat>\" value=\"<molString>\"> " +
"</object>";
shtml = shtml.Replace("<pixWidth>", pixWidth.ToString());
shtml = shtml.Replace("<pixHeight>", pixHeight.ToString());
if (useChimeString)
{
shtml = shtml.Replace("<molStringFormat>", "ChimeString");
shtml = shtml.Replace("<molString>", mol.GetChimeString());
}
else
{
shtml = shtml.Replace("<molStringFormat>", "MolfileString");
string mfs = mol.GetMolfileString();
if (mfs.Contains("\t")) // replace any tabs by a space
{
mfs = mfs.Replace("\t", " ");
}
shtml = shtml.Replace("<molString>", mfs);
}
string script = // set mol parameters
"<script language=\"JavaScript\"> " +
objId + ".Preferences.WedgeWidth = .3; " + // in .33 inch units
objId + ".Preferences.StandardBondLength = 144; " +
objId + ".Preferences.ColorAtomsByType = false; " +
objId + ".Preferences.HydrogenDisplayMode = 1; " + // 1= Hetero
objId + ".Preferences.ChemLabelFontString = \"Arial, 16\"; "; // make font larger
// New stero parameters
script +=
objId + ".Preferences.StereoAbsColorString = \"Black\"; " +
objId + ".Preferences.StereoAndColorString = \"Black\"; " +
objId + ".Preferences.StereoOrColorString = \"Black\"; " +
objId + ".Preferences.DisplayChiralStereoLabels = 2; " + // (On = 2, default is IUPAC = 0)
objId + ".Preferences.DisplayRS = true; " + // (default = false)
objId + ".Preferences.RLabelAtAbsCenter = \"R\"; " + // (default = "R")
objId + ".Preferences.RLabelAtAndCenter = \"\"; " + // (default = "R*")
objId + ".Preferences.RLabelAtOrCenter = \"\"; " + // (default = "(R)")
objId + ".Preferences.SLabelAtAbsCenter = \"S\"; " + // (default = "S")
objId + ".Preferences.SLabelAtAndCenter = \"\"; " + // (default = "S*")
objId + ".Preferences.SLabelAtOrCenter = \"\"; " + // (default = "(S)")
objId + ".Preferences.AbsStereoLabelText = \"\"; " + // (default = "")
objId + ".Preferences.AndStereoLabelText = \"\"; " + // (default = "AND Enantiomer")
objId + ".Preferences.OrStereoLabelText = \"\"; " + // (default = "OR Enantiomer")
objId + ".Preferences.MixedStereoLabelText = \"\"; "; // (default = "Mixed")
script += "</script> ";
shtml += " " + script;
html = "E <td>";
html_end = ""; // clear html to add to end
string label = mol.Caption;
if (label != null && label != "") // include compound number
{
txt = label;
if (txt.IndexOf("</") >= 0) // label contains already formatted html
{
txt2 = txt.Replace("</a>", "");
if (txt2 != txt) // move anchor close after structure to allow structure click
{
txt = txt2;
html_end = "</a>";
}
html += txt;
}
else // label contains a registry number possibly followed by other text, make regno an anchor
{
txt.Replace("\n", "<br>"); // change any newlines to breaks
for (i1 = 0; i1 < txt.Length; i1++) // look for end of regno
{
if (!Char.IsLetterOrDigit(txt[i1]) && txt[i1] != '-' && txt[i1] != ' ')
{
break;
}
}
if (i1 < txt.Length)
{
rntxt = txt.Substring(0, i1);
txt = txt.Substring(i1 + 1);
}
else
{
rntxt = txt;
txt = "";
}
string linkTag = "<a href=\"http://Mobius/command?ShowContextMenu:CompoundIdContextMenu:" + rntxt + "\">";
txt = // create a link to popup the regno operation menu
linkTag + rntxt + "</a>" + txt;
shtml = linkTag + shtml + "</a>"; // also include popup on structure
html += txt + "<br>";
}
}
html += "<center>" + shtml + "</center>" + html_end + "</td>\t";
Tb.Lines[r] += html; /* finish up & put in buffer */
return(html);
}
/// <summary>
/// Scale and translate structure and format into buffer
/// </summary>
/// <param name="mol">The structure</param>
/// <param name="cellStyle">Style/conditional formatting to apply to cell</param>
/// <param name="commandChar">Command character to use in buffer</param>
/// <param name="x">Coordinate of left side of structure</param>
/// <param name="width">Width of molecule box in milliinches</param>
/// <param name="r">Row in buffer to put on. If less than 0 then return formatted data</param>
/// <param name="heightInLines">number of lines used</param>
public FormattedFieldInfo FormatStructure(
MoleculeMx mol,
CellStyleMx cellStyle,
char commandChar,
int x,
int width,
int r,
ResultsField rfld = null,
DataRowMx dataRow = null)
{
Rectangle destRect, boundingRect;
int height; // formatted height in milliinches
bool markBoundaries;
int fixedHeight;
Bitmap bm;
Font font;
string txt, molfile, molString = "", svg, cid = null;
int translateType, desiredBondLength = 100;
int pixWidth = 0, pixHeight = 0;
bool debug = DataTableManager.DebugDetails;
if (debug)
{
DebugLog.Message("=============================== FormattingStructure ===============================");
}
PerformanceTimer pt = PT.Start("FormatStructure");
Stopwatch swTotal = Stopwatch.StartNew();
Stopwatch sw = Stopwatch.StartNew();
try
{
MoleculeFormat initialCsType = mol.PrimaryFormat;
string initialCsValue = mol.PrimaryValue;
QueryColumn qc = (rfld != null) ? rfld.QueryColumn : null;
FormattedFieldInfo ffi = new FormattedFieldInfo();
if (dataRow != null) // get any cid in row
{
int ki = DataTableManager.DefaultKeyValueVoPos;
if (ki < dataRow.Length)
{
cid = dataRow[ki] as string;
}
}
//DebugLog.Message("FormatStructure " + cid);
//if (!Rf.Grid) x = x; // debug
///////////////////////////////////
// Highlight structure
///////////////////////////////////
if (StructureHighlightPssc != null)
{
ParsedStructureCriteria pssc = StructureHighlightPssc;
// Hilight substructure search match
if (pssc.SearchType == StructureSearchType.Substructure || // regular SSS
pssc.SearchTypeUnion == StructureSearchType.Substructure) // handles related search for just SSS to get hilighting
{
if (HighlightStructureMatches)
{
try
{
mol = StrMatcher.HighlightMatchingSubstructure(mol);
if (DebugMx.False) // debug
{
//string highlightChildren = mol.MolLib.HighlightChildren;
//Color highlightColor = mol.MolLib.HighlightColor;
if (debug)
{
DebugLog.StopwatchMessage("tHilight", sw);
}
}
}
catch (Exception ex) { ex = ex; }
}
if (AlignStructureToQuery)
{
try
{
mol = StrMatcher.AlignToMatchingSubstructure(mol);
if (debug)
{
DebugLog.StopwatchMessage("tOrient", sw);
}
}
catch (Exception ex) { ex = ex; }
}
}
// Hilight SmallWorld structure match
else if (pssc.SearchType == StructureSearchType.SmallWorld) // Hilight SmallWorld structure search results
{
if (SmallWorldDepictions == null)
{
SmallWorldDepictions = new SmallWorldDepictions();
}
SmallWorldPredefinedParameters swp = pssc.SmallWorldParameters;
//DebugLog.Message("Depict " + cid + ", Hilight " + swp.Highlight + ", Align " + swp.Align); // + "\r\n" + new StackTrace(true));
if ((swp.Highlight || swp.Align) & Lex.IsDefined(cid)) // call depiction for these
{
svg = SmallWorldDepictions.GetDepiction(cid, swp.Highlight, swp.Align);
if (Lex.IsDefined(svg)) // have depiction?
{
{
pixWidth = MoleculeMx.MilliinchesToPixels(width);
bm = SvgUtil.GetBitmapFromSvgXml(svg, pixWidth);
ffi.FormattedBitmap = mol.FormattedBitmap = bm; // store in formatting info and chem structure
return(ffi);
}
}
else if (svg == null) // start retrieval of this decpiction type & fall through to get default structure initially
{
SmallWorldDepictions.StartDepictionRetrieval(Qm, StructureHighlightQc, swp.Highlight, swp.Align);
}
else
{
} // tried to get it but failed, fall through to get basic structure
}
}
else if (mol.AltFormDefined("Svg")) // svg form exist (e.g. SmallWorld or "related" structure search)?
{
svg = mol.SvgString;
if (Lex.IsDefined(svg))
{
pixWidth = MoleculeMx.MilliinchesToPixels(width);
bm = SvgUtil.GetBitmapFromSvgXml(svg, pixWidth);
ffi.FormattedBitmap = mol.FormattedBitmap = bm; // store in formatting info and chem structure
return(ffi);
}
}
}
///////////////////////////////////
// Handle each output device
///////////////////////////////////
ffi.HeightInLines = 1; // min of 1 line
if (Rf.SdFile)
{
FormatSdfileStructure(mol);
return(null);
}
int pageHeight = 11000;
if (Rf.PageMargins != null)
{
pageHeight = Rf.PageMargins.Top + Rf.PageHeight + Rf.PageMargins.Bottom;
}
if (Rf.Excel || Rf.Word)
{
translateType = 2;
}
else
{
translateType = 0;
}
if (!Rf.FixedHeightStructures)
{
fixedHeight = 0; // not fixed height
}
else if (Rf.Excel || Rf.Word)
{
fixedHeight = 1; // always fixed height
}
else
{
fixedHeight = 2; // fixed height unless need to expand
}
if (Rf.Word && Rf.FixedHeightStructures)
{
markBoundaries = true;
}
else
{
markBoundaries = false;
}
destRect = new Rectangle(0, 0, width, width * 4 / 5); // default dest rect
///////////////////////////////////////////////////////////////////////////
// Tempory fake generation of HELM & associatedimage for biopolymer testing
///////////////////////////////////////////////////////////////////////////
//if (MoleculeMx.HelmEnabled == DebugMx.False) // artificially generate helm molecules
// MoleculeMx.SetMoleculeToTestHelmString(mol.GetCorpId().ToString(), mol);
///////////////////////////////////////////////////////////////////////////
// End of tempory fake generation of HELM & associatedimage for biopolymer testing
///////////////////////////////////////////////////////////////////////////
bool fitStructure = true;
if (mol.IsChemStructureFormat)
{
if (Rf.Grid) // special scale for grid
{
double scale = (float)width / MoleculeMx.StandardBoxWidth;
desiredBondLength = mol.CdkMol.AdjustBondLengthToValidRange((int)(MoleculeMx.StandardBondLength * scale));
//desiredBondLength = (int)(ChemicalStructure.StandardBondLength * (Rf.PageScale / 100.0));
desiredBondLength = (int)(desiredBondLength * 90.0 / 100.0); // scale down a bit for grid
if (debug)
{
DebugLog.StopwatchMessage("tAdjustBondLength1", sw);
}
}
else // set desired bond length based on page scaling
{
float scale = (float)width / MoleculeMx.StandardBoxWidth;
desiredBondLength = mol.CdkMol.AdjustBondLengthToValidRange((int)(MoleculeMx.StandardBondLength * scale));
//desiredBondLength = (int)(ChemicalStructure.StandardBondLength * (Rf.PageScale / 100.0));
if (debug)
{
DebugLog.StopwatchMessage("tAdjustBondLength2", sw);
}
}
if (desiredBondLength < 1)
{
desiredBondLength = 1;
}
if (debug)
{
DebugLog.StopwatchMessage("tBeforeFit", sw);
}
if (fitStructure)
{
mol.CdkMol.FitStructureIntoRectangle // scale and translate structure into supplied rectangle.
(ref destRect, desiredBondLength, translateType, fixedHeight, markBoundaries, pageHeight, out boundingRect);
}
if (debug)
{
DebugLog.StopwatchMessage("tFitStructure", sw);
}
ffi.HeightInLines = (int)(destRect.Height / Rf.LineHeight + 1); // lines needed
}
else if (mol.IsBiopolymerFormat)
{
if (mol.PrimaryFormat == MoleculeFormat.Helm && Rf.Excel)
{
svg = HelmControl.GetSvg(mol.HelmString);
float inchWidth = width / 1000.0f; // convert width milliinches to inches
Svg.SvgDocument svgDoc = SvgUtil.AdjustSvgDocumentToFitContent(svg, inchWidth, Svg.SvgUnitType.Inch);
RectangleF svgbb = svgDoc.Bounds;
float ar = svgbb.Width / svgbb.Height; // aspect ratio of svg bounding box
height = (int)(width / ar); // height in milliinches
ffi.HeightInLines = (int)(height / Rf.LineHeight) + 1; // lines needed
destRect = new Rectangle(0, 0, width, height);
}
}
//////////////////////////
/// Output to Grid
//////////////////////////
if (Rf.Grid)
{
pixWidth = MoleculeMx.MilliinchesToPixels(destRect.Width);
pixHeight = MoleculeMx.MilliinchesToPixels(destRect.Height);
if (cellStyle == null)
{
if (Qm == null || Qm.MoleculeGrid == null)
{
font = new Font("Tahoma", 8.25f);
}
else
{
font = new Font(Qm.MoleculeGrid.Font, FontStyle.Underline);
}
cellStyle = new CellStyleMx(font, Color.Blue, Color.Empty);
}
if (mol.IsChemStructureFormat) // molfile type molecule
{
if (debug)
{
DebugLog.StopwatchMessage("tBeforeGetDisplayPreferences", sw);
}
DisplayPreferences dp = mol.GetDisplayPreferences();
if (debug)
{
DebugLog.StopwatchMessage("tGetDisplayPreferences", sw);
}
//desiredBondLength = mol.CdkMol.AdjustBondLengthToValidRange(desiredBondLength); // be sure bond len within allowed range
//if (debug) DebugLog.StopwatchMessage("tAdjustBondLengthToValidRange", sw);
//dp.StandardBondLength = MoleculeMx.MilliinchesToDecipoints(desiredBondLength);
bm = mol.CdkMol.GetFixedHeightMoleculeBitmap(pixWidth, pixHeight, dp, cellStyle, mol.Caption);
if (debug)
{
DebugLog.StopwatchMessage("tGetBitmap", sw);
}
}
else if (mol.IsBiopolymerFormat) // Output HELM image for biopolymer
{
pixWidth = MoleculeMx.MilliinchesToPixels(width);
bm = HelmConverter.HelmToBitmap(mol, pixWidth);
}
else
{
bm = new Bitmap(1, 1);
}
ffi.FormattedBitmap = mol.FormattedBitmap = bm; // store in formatting & structure
ffi.FormattedText = "Formatted"; // indicate formatted (could save structure string but not needed and avoids possible conversion overhead)
return(ffi);
}
//////////////////////////
/// Output to Html
//////////////////////////
else if (Rf.Html)
{
if (r >= 0)
{
AssureTbFree(0, r + ffi.HeightInLines - 1);
}
if (mol.IsChemStructureFormat)
{
FormatChemStructureHtml(mol, destRect, width, r);
}
else if (mol.IsBiopolymerFormat)
{
FormatBiopolymerStructureHtml(mol, destRect, width, r);
}
if (debug)
{
DebugLog.StopwatchMessage("tFormatHtmlStructure", sw);
}
ffi.FormattedBitmap = mol.FormattedBitmap;
ffi.FormattedText = mol.FormattedText;
return(ffi);
}
/////////////////////////////////////////////////////////////////
/// Other format, store Smiles or Helm & any cellStyle in buffer
/////////////////////////////////////////////////////////////////
else
{
if (mol.IsChemStructureFormat)
{
if (Rf.ExportStructureFormat == ExportStructureFormat.Smiles)
{
molString = mol.GetSmilesString();
}
else
{
molString = mol.GetChimeString(); // use Chime if not smiles
}
}
else if (mol.IsBiopolymerFormat)
{
molString = mol.PrimaryValue; // usually Helm but could be sequence
}
txt = String.Format("{0} {1} {2} {3} {4} {5} {6}",
x, width, destRect.Left, destRect.Top, destRect.Right, destRect.Bottom, molString);
if (cellStyle != null) // apply style to cell?
{
txt += " <CellStyle " + cellStyle.Serialize() + ">";
}
txt = commandChar + " " + txt + "\t";
if (r >= 0)
{
AssureTbFree(0, r + ffi.HeightInLines - 1);
Tb.Lines[r] += txt; // put in buffer
}
else
{
return(new FormattedFieldInfo(txt)); // just return formatting
}
}
return(null);
}
catch (Exception ex)
{
DebugLog.Message(DebugLog.FormatExceptionMessage(ex));
return(null);
}
finally
{
pt.Update();
int formatCount = pt.Count;
//ClientLog.Message(pt.ToString() + ", " + cs.GetMolHeader()[2]); // + ", " + new StackTrace(true));
if (debug)
{
DebugLog.StopwatchMessage("tTotalTime", swTotal);
}
}
}
/// <summary>
/// OK button clicked, process input
/// </summary>
/// <returns></returns>
DialogResult ProcessInput()
{
int rgCount; // number of Rgroups
List <Rgroup> rgList; // list of existing Rgroups
bool[] rgExists; // entry = true if rgroup exists in core
Rgroup rg;
bool oneD, twoD; // matrix dimensionality
List <string> keys = null;
Dictionary <string, List <QualifiedNumber> > mElem; // matrix element dictionary
List <RgroupSubstituent>[] rSubs; // substituents seen for each Rgroup
Query q, q0, q2;
QueryTable qt, qt2;
QueryColumn qc, qc2;
MetaTable mt, mt2;
MetaColumn mc, mc2;
DataTableMx dt;
DataRowMx dr;
DialogResult dlgRslt;
string tok;
int ri, rii, si, qti, qci, bi, bi2;
// Get core structure & list of R-groups
MoleculeMx core = new MoleculeMx(MoleculeFormat.Molfile, SQuery.MolfileString);
if (core.AtomCount == 0)
{
MessageBoxMx.ShowError("A Core structure with R-groups must be defined");
return(DialogResult.None);
}
if (!Structure.Checked && !Smiles.Checked && !Formula.Checked &&
!Weight.Checked && !Index.Checked)
{
MessageBoxMx.ShowError("At least one substituent display format must be selected.");
return(DialogResult.None);
}
mt = MetaTableCollection.GetWithException("Rgroup_Decomposition");
qt = new QueryTable(mt);
qc = qt.GetQueryColumnByNameWithException("Core");
qc.MolString = core.GetMolfileString(); // put core structure into table criteria
qc.CriteriaDisplay = "Substructure search (SSS)";
qc.Criteria = "CORE SSS SQUERY";
qc = qt.GetQueryColumnByNameWithException("R1_Structure");
if (ShowCoreStructure.Checked)
{
qc.Label = "R-group, Core\tChime=" + core.GetChimeString(); // reference core in query col header label
qc.MetaColumn.Width = 25;
}
RgroupDecomposition.SetSelected(qt, "R1_Structure", Structure.Checked); // select for retrieval if checked
RgroupDecomposition.SetSelected(qt, "R1_Smiles", Smiles.Checked);
RgroupDecomposition.SetSelected(qt, "R1_Formula", Formula.Checked);
RgroupDecomposition.SetSelected(qt, "R1_Weight", Weight.Checked);
RgroupDecomposition.SetSelected(qt, "R1_SubstNo", Index.Checked);
string terminateOption = "First mapping"; // terminate on first complete match
qc = qt.GetQueryColumnByNameWithException("Terminate_Option");
qc.Criteria = qt.MetaTable.Name + " = " + Lex.AddSingleQuotes(terminateOption);
qc.CriteriaDisplay = "= " + Lex.AddSingleQuotes(terminateOption);
QueryTable rgdQt = qt; // keep a ref to it
if (QbUtil.Query == null || QbUtil.Query.Tables.Count == 0)
{
MessageBoxMx.ShowError("No current query.");
return(DialogResult.None);
}
q0 = QbUtil.Query; // original query this analysis is based on
q = q0.Clone(); // make copy of source query we can modify
q.SingleStepExecution = false;
qti = 0;
while (qti < q.Tables.Count) // deselect query columns that we don't want
{
qt = q.Tables[qti];
if (Lex.Eq(qt.MetaTable.Name, "Rgroup_Decomposition"))
{ // remove any rgroup decomp table
qti++;
continue;
}
mt = qt.MetaTable;
if (mt.MultiPivot || // check for tables not allowed in underlying query
mt.MetaBrokerType == MetaBrokerType.CalcField || // (called ShouldPresearchAndTransform previously)
mt.MetaBrokerType == MetaBrokerType.MultiTable ||
mt.MetaBrokerType == MetaBrokerType.RgroupDecomp)
{
MessageBoxMx.ShowError("Multipivot/Rgroup table \"" + qt.ActiveLabel +
"\" can't be included in an underlying Rgroup Matrix query");
return(DialogResult.None);
}
for (qci = 0; qci < qt.QueryColumns.Count; qci++)
{
qc = qt.QueryColumns[qci];
if (qc.MetaColumn == null)
{
continue;
}
switch (qc.MetaColumn.DataType)
{
case MetaColumnType.CompoundId: // keep only these
case MetaColumnType.Integer:
case MetaColumnType.Number:
case MetaColumnType.QualifiedNo:
case MetaColumnType.String:
break;
default:
qc.Selected = false;
break;
}
}
qti++;
}
q.AddQueryTable(rgdQt); // Add Rgroup decom table to end of cloned source query
Progress.Show("Retrieving data...");
try
{
dlgRslt = ToolHelper.ExecuteQuery(ref q, out keys);
if (dlgRslt != DialogResult.OK)
{
return(dlgRslt);
}
}
catch (Exception ex)
{
MessageBoxMx.ShowError("Error executing query:\r\n" + ex.Message);
return(DialogResult.None);
}
if (keys == null || keys.Count == 0)
{
Progress.Hide();
MessageBoxMx.ShowError("No results were returned by the query.");
return(DialogResult.None);
}
// Scan modified query to get list of rgroup indexes that are present
rgExists = new bool[32];
rgList = new List <Rgroup>();
QueryTable rgQt = q.GetQueryTableByName("Rgroup_Decomposition");
foreach (QueryColumn qc0 in rgQt.QueryColumns)
{
mc = qc0.MetaColumn;
if (!(mc.Name.StartsWith("R") && mc.Name.EndsWith("_STRUCTURE") && qc0.Selected))
{
continue; // skip if not a selected Rgroup structure
}
int len = mc.Name.Length - ("R" + "_STRUCTURE").Length;
tok = mc.Name.Substring(1, len);
if (!int.TryParse(tok, out ri))
{
continue;
}
rgExists[ri - 1] = true;
rg = new Rgroup();
rg.RIndex = ri;
rg.VoPos = qc0.VoPosition;
rgList.Add(rg);
}
for (bi = 1; bi < rgList.Count; bi++)
{ // sort by increasing R index
rg = rgList[bi];
for (bi2 = bi - 1; bi2 >= 0; bi2--)
{
if (rg.RIndex >= rgList[bi2].RIndex)
{
break;
}
rgList[bi2 + 1] = rgList[bi2];
}
rgList[bi2 + 1] = rg;
}
rgCount = rgList.Count;
twoD = TwoD.Checked;
if (rgCount == 1)
{
twoD = false; // if only 1 rgroup can't do as 2d
}
oneD = !twoD;
// Read data into mElem and rgroup substituents into rSubs.
// Matrix mElem is keyed on [R1Smiles, R2Smiles,... RnSmiles, FieldName] for 1d and
// [R1Smiles, R2Smiles,... FieldName, RnSmiles] for 2d
QueryManager qm = q.QueryManager as QueryManager;
DataTableManager dtm = qm.DataTableManager;
dt = qm.DataTable;
mElem = new Dictionary <string, List <QualifiedNumber> >(); // matrix element dictionary
rSubs = new List <RgroupSubstituent> [32]; // list of substituents seen for each Rgroup
for (rii = 0; rii < rgCount; rii++) // alloc substituent list for rgroup
{
rSubs[rii] = new List <RgroupSubstituent>();
}
int rowCount = 0;
while (true)
{ // scan data accumulating rgroup substituents and data values
dr = dtm.FetchNextDataRow();
if (dr == null)
{
break;
}
rowCount++;
string cid = dr[dtm.KeyValueVoPos] as string;
string lastMapCid = "", rgroupKey = "", rgroupKeyLast = "";
int mapCount = 0;
for (rii = 0; rii < rgCount; rii++) // for
{
MoleculeMx rSub = dr[rgList[rii].VoPos] as MoleculeMx;
if (rSub == null || rSub.AtomCount == 0)
{
continue;
}
ri = rgList[rii].RIndex; // actual R index in query
int subIdx = RgroupSubstituent.Get(rSub, rSubs[rii]);
// if (ri == 1 && subIdx != 0) subIdx = subIdx; // debug
if (subIdx < 0)
{
continue;
}
string rKey = "R" + ri.ToString() + "_" + (subIdx + 1).ToString();
if (oneD || rii < rgCount - 1)
{
if (rgroupKey != "")
{
rgroupKey += "\t";
}
rgroupKey += rKey;
}
else
{
rgroupKeyLast = rKey;
}
lastMapCid = cid;
mapCount++;
}
if (lastMapCid == cid) // add the data if compound has a mapping
{
AccumulateMatrixElements(mElem, q, dr, rgroupKey, rgroupKeyLast, cid);
}
if (Progress.IsTimeToUpdate)
{
Progress.Show("Retrieving data: " + StringMx.FormatIntegerWithCommas(rowCount) + " rows...");
}
}
if (rowCount == 0)
{
Progress.Hide();
MessageBoxMx.ShowError("No data rows retrieved");
return(DialogResult.None);
}
if (twoD && (rSubs[rgCount - 1] == null || rSubs[rgCount - 1].Count == 0))
{ // if 2D be sure we have at least one substituent for the last Rgroup
Progress.Hide();
MessageBoxMx.ShowError("No substituents found for R" + rgCount.ToString());
return(DialogResult.None);
}
// Create a MetaTable & DataTable for matrix results
Progress.Show("Analyzing data...");
mt = new MetaTable(); // create output table
MatrixCount++;
mt.Name = "RGROUPMATRIX_" + MatrixCount;
mt.Label = "R-group Matrix " + MatrixCount;
mt.MetaBrokerType = MetaBrokerType.RgroupDecomp;
mc = // use sequence for key
mt.AddMetaColumn("RgroupMatrixId", "No.", MetaColumnType.Integer, ColumnSelectionEnum.Selected, 3);
mc.ClickFunction = "None"; // avoid hyperlink on this key
mc.IsKey = true;
int maxLeftR = rgCount;
if (twoD)
{
maxLeftR = rgCount - 1;
}
for (ri = 0; ri < maxLeftR; ri++)
{
string rStr = "R" + (ri + 1).ToString();
if (Structure.Checked)
{
mc = mt.AddMetaColumn(rStr + "Str", rStr, MetaColumnType.Structure, ColumnSelectionEnum.Selected, 12);
if (ri == 0 && ShowCoreStructure.Checked) // include core structure above R1 if requested
{
string chimeString = MoleculeMx.MolfileStringToSmilesString(SQuery.MolfileString);
mc.Label = "R1, Core\tChime=" + chimeString;
mc.Width = 25;
}
}
if (Smiles.Checked)
{
mc = mt.AddMetaColumn(rStr + "Smi", rStr + " Smiles", MetaColumnType.String, ColumnSelectionEnum.Selected, 12);
}
if (Formula.Checked)
{
mc = mt.AddMetaColumn(rStr + "Mf", rStr + " Formula", MetaColumnType.String, ColumnSelectionEnum.Selected, 8);
}
if (Weight.Checked)
{
mc = mt.AddMetaColumn(rStr + "MW", rStr + " Mol. Wt.", MetaColumnType.Number, ColumnSelectionEnum.Selected, 6, ColumnFormatEnum.Decimal, 2);
}
if (Index.Checked)
{
mc = mt.AddMetaColumn(rStr + "Index", rStr + " Subst. Idx.", MetaColumnType.Number, ColumnSelectionEnum.Selected, 4);
mc.Format = ColumnFormatEnum.Decimal;
}
}
mc = // add column to contain result type
mt.AddMetaColumn("ResultType", "Result Type", MetaColumnType.String, ColumnSelectionEnum.Selected, 12);
if (oneD) // add just 1 column to contain results
{
mc = mt.AddMetaColumn("Results", "Results", MetaColumnType.QualifiedNo, ColumnSelectionEnum.Selected, 12);
mc.MetaBrokerType = MetaBrokerType.RgroupDecomp; // broker to do special col handling for cond formtting
if (QbUtil.Query.UserObject.Id > 0)
{
mc.DetailsAvailable = true;
}
}
else // add col for each substituent for last rgroup
{
string rStr = "R" + rgCount.ToString();
for (si = 0; si < rSubs[rgCount - 1].Count; si++)
{
string cName = rStr + "_" + (si + 1).ToString();
string cLabel = cName.Replace("_", ".");
RgroupSubstituent rgs = rSubs[ri][si]; // get substituent info
if (Structure.Checked) // include structure
{
cLabel += "\tChime=" + rgs.Struct.GetChimeString();
}
else if (Smiles.Checked)
{
cLabel += " = " + rgs.Struct.GetSmilesString();
}
else if (Formula.Checked)
{
cLabel += " = " + rgs.Struct.MolFormula;
}
else if (Weight.Checked)
{
cLabel += " = " + rgs.Struct.MolWeight;
}
else if (Index.Checked)
{
cLabel += " = " + (si + 1).ToString();
}
mc = mt.AddMetaColumn(cName, cLabel, MetaColumnType.QualifiedNo, ColumnSelectionEnum.Selected, 12);
mc.MetaBrokerType = MetaBrokerType.RgroupDecomp;
if (QbUtil.Query.UserObject.Id > 0)
{
mc.DetailsAvailable = true;
}
}
}
MetaTableCollection.UpdateGlobally(mt); // add as a known metatable
if (mElem.Count == 0) // be sure we have a matrix
{
Progress.Hide();
MessageBoxMx.ShowError("No matrix can be created because insufficient data was found.");
return(DialogResult.None);
}
// Build the DataTable
Progress.Show("Building data table...");
q2 = new Query(); // build single-table query to hold matrix
qt2 = new QueryTable(q2, mt);
dt = DataTableManager.BuildDataTable(q2);
Dictionary <string, List <QualifiedNumber> > .KeyCollection kc = mElem.Keys;
string[] rgKeys = new string[mElem.Count];
kc.CopyTo(rgKeys, 0);
Array.Sort(rgKeys);
string[] rgKey = null, lastRgKey = null;
int rki = 0;
for (rki = 0; rki < rgKeys.Length; rki++)
{
rgKey = rgKeys[rki].Split('\t');
int riTop = rgCount + 1; // all r substituents & field name on left
if (twoD)
{
riTop = rgCount;
}
for (ri = 0; ri < riTop; ri++) // see if any changes in left side substituents or field name
{
if (lastRgKey == null || rgKey[ri] != lastRgKey[ri])
{
break;
}
}
if (ri < riTop || oneD) // if 2d then new row only if some change before last R
{
dr = dt.NewRow();
dt.Rows.Add(dr);
dr[dtm.KeyValueVoPos + 1] = new NumberMx(dt.Rows.Count); // integer row key
}
if (!HideRepeatingSubstituents.Checked)
{
ri = 0; // start at first if not hiding
}
lastRgKey = rgKey;
for (ri = ri; ri < riTop; ri++) // build row with these
{
string rgSub = rgKey[ri]; // get substituent id or table.column name
if (rgSub == "")
{
continue;
}
if (ri < riTop - 1)
{ // output substituent and/or smiles
string rStr = "R" + (ri + 1).ToString();
si = rgSub.IndexOf("_");
si = Int32.Parse(rgSub.Substring(si + 1)) - 1; // get substituent index
RgroupSubstituent rgs = rSubs[ri][si]; // get substituent info
if (Structure.Checked)
{
qc2 = qt2.GetQueryColumnByName(rStr + "Str");
dr[QcToDcName(qc2)] = rgs.Struct;
}
if (Smiles.Checked)
{
qc2 = qt2.GetQueryColumnByName(rStr + "Smi");
dr[QcToDcName(qc2)] = new StringMx(rgs.Struct.GetSmilesString());
}
if (Formula.Checked)
{
qc2 = qt2.GetQueryColumnByName(rStr + "Mf");
dr[QcToDcName(qc2)] = new StringMx(rgs.Struct.MolFormula);
}
if (Weight.Checked)
{
qc2 = qt2.GetQueryColumnByName(rStr + "Mw");
dr[QcToDcName(qc2)] = new NumberMx(rgs.Struct.MolWeight);
}
if (Index.Checked)
{
qc2 = qt2.GetQueryColumnByName(rStr + "Index");
dr[QcToDcName(qc2)] = new NumberMx(si + 1);
}
}
else // output field name
{
string[] sa = rgSub.Split('.'); // get field name
qt = q.GetQueryTableByName(sa[0]);
qc = qt.GetQueryColumnByName(sa[1]);
string fieldName = qc.ActiveLabel;
if (q0.Tables.Count >= 3) // qualify by table if 3 or more tables in original query
{
fieldName = qt.ActiveLabel + " - " + fieldName;
}
qc2 = qt2.GetQueryColumnByName("ResultType");
dr[QcToDcName(qc2)] = new StringMx(fieldName);
}
}
// Output value
string cName;
if (oneD)
{
cName = "Results";
}
else
{
cName = rgKey[rgCount]; // get key for this substituent (e.g. R2_1)
}
if (Lex.IsUndefined(cName))
{
continue; // may be no substituent match
}
qc2 = qt2.GetQueryColumnByName(cName);
QualifiedNumber qn = SummarizeData(mElem[rgKeys[rki]]); // get summarized value
dr[QcToDcName(qc2)] = qn;
}
ToolHelper.DisplayData(q2, dt, true);
UsageDao.LogEvent("RgroupMatrix");
Progress.Hide();
return(DialogResult.OK);
}
/// <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;
}