/// <summary>
/// Format structure for output to SDFile
/// </summary>
/// <param name="molid"></param>
void FormatSdfileStructure(
MoleculeMx cs)
{
string molFile, cid;
if (SS.I.RemoveLeadingZerosFromCids) // normal formatting
{
cid = CompoundId.Format(CurrentKey);
}
else
{
cid = CurrentKey; // just use internal formatting
}
cs = cs.Convert(Rf.StructureFlags | MoleculeTransformationFlags.RemoveStructureCaption, cid);
molFile = cs.GetMolfileString();
if (molFile.IndexOf("\r") < 0) // add carriage returns to molfile if it doesn't contain them
{
molFile = molFile.Replace("\n", "\r\n");
}
SdfLine = molFile;
return;
}
// # Get list of bits where at least one must be in result fp. Use least popular bits if possible.
// if db.mfp_counts:
// reqbits = [count['_id'] for count in db.mfp_counts.find({'_id': {'$in': qfp
// }
//}).sort('count', 1).limit(ncommon)]
// else:
// reqbits = qfp[:ncommon]
// results = []
// for fp in db.molecules.find({'mfp.bits': {'$in': reqbits}, 'mfp.count': {'$gte': qmin, '$lte': qmax}}):
// intersection = len(set(qfp) & set(fp['mfp']['bits']))
// pn = fp['mfp']['count']
// tanimoto = float(intersection) / (pn + qn - intersection)
// if tanimoto >= threshold:
// results.append((tanimoto, fp['chembl_id'], fp['smiles']))
// return results
/// <summary>
/// Test to calculate similarity between pairs of structures (Alt syntax: Call SimSearchMx.Test [cid1] [cid2]
/// Tautomers:
/// Isotopes:
/// Neg Counterion, (Cl-) with 2 quatternary N+ with H attached in main frag:
/// Neg Counterion, (I-) with quatternary N+ (no attached H) in main frag:
/// Pos Counterion (Li+) with O- in main frag:
/// Benzene, cyclohexane:
/// StereoIsomers:
/// StereoIsomers:
/// </summary>
/// <param name="args"></param>
/// <returns></returns>
public static string Test(string args)
{
string[] sa = args.Split(' ');
string cid1 = CompoundId.Normalize(sa[0]);
string cid2 = CompoundId.Normalize(sa[1]);
int smiLen = 40;
MoleculeMx s1 = MoleculeMx.SelectMoleculeForCid(cid1);
IAtomContainer mol = CdkMol.MolfileToAtomContainer(s1.GetMolfileString());
UniChemData ucd1 = UniChemUtil.BuildUniChemData(mol);
List <FingerprintMx> fps1 = UniChemDataToFingerprintMxList(ucd1);
MoleculeMx s2 = MoleculeMx.SelectMoleculeForCid(cid2);
IAtomContainer mol2 = CdkMol.MolfileToAtomContainer(s2.GetMolfileString());
UniChemData ucd2 = UniChemUtil.BuildUniChemData(mol2);
List <FingerprintMx> fps2 = UniChemDataToFingerprintMxList(ucd2);
string fps2Smiles = (sa[0] + " / " + sa[1]).PadRight(smiLen);
string scores = "";
for (int i1 = 0; i1 < fps1.Count; i1++)
{
FingerprintMx fp1 = fps1[i1];
for (int i2 = 0; i2 < fps2.Count; i2++)
{
FingerprintMx fp2 = fps2[i2];
if (i1 == 0) // build smiles headers of cid2 frags if first cid1 frag
{
fps2Smiles += "\t" + fp2.CanonSmiles.PadRight(smiLen);
}
if (i2 == 0)
{
scores += "\r\n" + fp1.CanonSmiles.PadRight(smiLen); // include smiles at start of each line
}
float simScore = CalculateFingerprintPairSimilarityScore(fp1, fp2);
scores += "\t" + string.Format("{0:0.00}", simScore).PadRight(smiLen);
}
}
scores = fps2Smiles + scores;
FileUtil.WriteAndOpenTextDocument("SimilarityScores", scores);
return("");
}
/// <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>
/// 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);
}
/// Insert Insight for Excel structure
public static void SetInsightForExcelMolecule(
int row,
int col,
MoleculeMx mol)
{
if (LogCalls)
{
DebugLog.Message("ExcelOp SetInsightForExcelMolecule " + row + ", " + col);
}
if (StructureInsertCount == 0) // check that AddIn is loaded
{
InsightForExcelAddInLoaded = LoadInsightForExcelAddIn();
if (!InsightForExcelAddInLoaded)
{
DebugLog.Message("Insight Chemistry AddIn failed to load");
}
}
StructureInsertCount++;
try
{
if (MoleculeMx.IsUndefined(mol))
{
return;
}
string molFile = mol.GetMolfileString();
if (!InsightForExcelAddInLoaded)
{
throw new Exception("Insight Chemistry AddIn failed to load");
}
CellSelect(row, col); // outputCell
string errorString = "";
bool returnStatus = false;
string textFormat = "Automatic";
string macroPath = "InsightChemistry.xlam!IxlPutChemistryInCell"; // path to macro (don't use fullPath = XlApp.LibraryPath + @"\" + "InsightChemistry.xlam!IxlPutChemistryInCell")
string fullPath = XlApp.LibraryPath + @"\" + macroPath; // (do not use full path)
//if (StructureInsertCount == 2) throw new Exception("Test Exception"); // debug
object ro = XlApp.Run( // call Insight macro directly (i.e. no added VBA macro in sheet)
Macro: macroPath,
Arg1: molFile,
Arg2: XlRange,
Arg3: errorString,
Arg4: returnStatus,
Arg5: textFormat);
ReleaseObject(ro);
return;
}
catch (Exception ex)
{
string msg = ex.Message;
try
{
msg =
"Insight for Excel Failed\r\n" +
"Molecule: " + StructureInsertCount + ", Atoms: " + mol.AtomCount;
XlSheet.Cells[row, col] = msg;
}
catch (Exception ex2) { ex2 = ex2; }
throw new Exception(msg, ex); // throw exception so failure gets counted
}
}
/// <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>
/// Handle conversion of Mobius custom data types between the grid and the underlying DataSet
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
void ProcessCustomUnboundColumnDataEvent(object sender, CustomColumnDataEventArgs e)
{
MobiusDataType mdt = null;
FormattedFieldInfo ffi = null;
bool formatted = false;
NumberMx numberEx;
StringMx stringEx;
ImageMx imageMx;
DateTimeMx dateTimeEx;
DataRowMx dr = null;
BandedGridView mbgv;
int nonNullDri;
string debugMsg;
if (DebugMx.False) // fillValuesImmediately debug test
{
e.Value = "XXX";
return;
}
DateTime t0 = DateTime.Now;
int callId = ++UnboundCalls; // get id for this call
if (sender is BandedGridView)
{
mbgv = sender as BandedGridView;
}
if (Grid.DataSource == null)
{
return;
}
CellInfo ci = Grid.GetDataTableCellInfo(e.ListSourceRowIndex, e.Column);
//if (e.ListSourceRowIndex == 2 && ci.DataRowIndex == 1) e = e; // debug
//if (ci.Mc.DataType == MetaColumnType.CompoundId && ci.DataRowIndex > 0) ci = ci; // debug
//DebugLog.Message("CustomUnboundColumnData " + ci.DataRowIndex + ", " + ci.DataColIndex + ", " + ci.DataValue.ToString());
if (ci.Rfld == null)
{
return;
}
QueryManager qm = Grid.QueryManager;
ResultsFormatter fmtr = qm.ResultsFormatter;
ResultsFormat rf = qm.ResultsFormat;
if (e.ListSourceRowIndex == GridControl.NewItemRowHandle || e.ListSourceRowIndex >= Qm.DataTable.Rows.Count) // new row being created
{
if (NewRow == null)
{
NewRow = Qm.DataTable.NewRow();
}
dr = NewRow;
}
else if (e.ListSourceRowIndex >= 0 && ci.DataRowIndex >= 0) // row exist in DataTable (i.e. not new row)
{
AdjustDataRowToRender(ci);
if (ci.DataRowIndex >= 0)
{
dr = DataTable.Rows[ci.DataRowIndex];
if (ci.DataRowIndex == 0)
{
}
}
}
else
{
if (DebugDetails)
{
ClientLog.Message("Fail 1");
}
return; // something else, ignore
}
// Store edited data for unbound column in DataTable
if (e.IsSetData)
{
SetGridData(e, ci);
return;
}
else if (!e.IsGetData)
{
return; // just return if not GetData as expected
}
// Get data from underlying unbound dataset & return in format for grid
//if (ci.Mc.DataType == MetaColumnType.Structure) ci = ci; // debug
//if (ci.Mc.DataType == MetaColumnType.String) ci = ci; // debug
//if (ci.DataValue is StringEx && ((StringEx)ci.DataValue).Value == " ") ci = ci; // debug
UnboundGets++;
if (dr == null)
{
e.Value = null;
if (DebugDetails)
{
ClientLog.Message("Fail 2"); // debug
}
return;
}
if (Dtm.IsRetrievingDataMessageRow(dr) && ci.Mc != null && !ci.Mc.IsGraphical)
{
//if (ci.Mc.IsKey) // show retrieving data message for key field
e.Value = "Retrieving data...";
return;
}
object fieldValue = dr[ci.DataColIndex];
if (DebugDetails && fieldValue is MoleculeMx) // debug
{
MoleculeMx cs = fieldValue as MoleculeMx;
MoleculeFormat csType = cs.PrimaryFormat;
string csValue = cs.PrimaryValue;
int csLen = cs.PrimaryValue.Length;
string molfile = cs.GetMolfileString();
molfile = molfile;
}
try
{
// If already formatted use existing formatting info
ffi = null;
if (fieldValue is MobiusDataType)
{
mdt = (MobiusDataType)fieldValue;
if (mdt.FormattedBitmap != null)
{
ffi = new FormattedFieldInfo();
ffi.FormattedBitmap = mdt.FormattedBitmap;
}
else if (mdt.FormattedText != null)
{
ffi = new FormattedFieldInfo();
ffi.FormattedText = mdt.FormattedText;
}
if (ffi != null) // if formatted then copy other format attributes as well
{
ffi.BackColor = mdt.BackColor;
ffi.ForeColor = mdt.ForeColor;
ffi.Hyperlink = mdt.Hyperlink;
}
}
// If not formatted then format
if (ffi == null) // need to format?
{
// Format non-image field (including structures)
if (ci.Mc.DataType != MetaColumnType.Image) // format other than image immediately
{
//if (ci.Mc.DataType == MetaColumnType.Structure) // debug
//{
// DebugLog.Message(fieldValue.ToString());
// UIMisc.Beep();
//}
ffi = fmtr.FormatField(ci.Rt, ci.TableIndex, ci.Rfld, ci.FieldIndex, dr, e.ListSourceRowIndex, fieldValue, ci.DataRowIndex, false);
FormatFieldCalls++;
if (ci.Mc.DataType == MetaColumnType.Structure)
{
FormatStructureFieldCalls++;
}
StoreFormattingInformationInMdt(ffi, fieldValue, dr, ci, mdt);
formatted = true;
}
// Image: start asynch call to get image in background as necessary since it is too slow to wait for it here
else
{
if (fieldValue is ImageMx)
{
imageMx = fieldValue as ImageMx;
}
else
{
imageMx = new ImageMx();
if (fieldValue != null)
{
if (fieldValue is MobiusDataType)
{
imageMx.DbLink = (fieldValue as MobiusDataType).DbLink;
}
else
{
imageMx.DbLink = fieldValue.ToString(); // store field value as dblink
}
}
dr.ItemArrayRef[ci.DataColIndex] = imageMx; // store new image object without firing event
}
mdt = imageMx; // copy image object to general MobiusDataType
ffi = new FormattedFieldInfo();
if (imageMx.FormattedBitmap != null) // already have bitmap?
{
ffi.FormattedBitmap = imageMx.FormattedBitmap;
}
else if (imageMx.Value != null) // have the bitmap, just need to scale it
{
int fieldWidth = ci.Rfld.FieldWidth; // current field width in milliinches
int desiredWidth = (int)((fieldWidth / 1000.0) * GraphicsMx.LogicalPixelsX * 1.0); // width in pixels
imageMx.FormattedBitmap = BitmapUtil.ScaleBitmap(imageMx.Value, desiredWidth);
ffi.FormattedBitmap = imageMx.FormattedBitmap;
}
else if (imageMx.IsRetrievingValue) // already retrieving?
{
ffi.FormattedBitmap = (Bitmap)RetrievingImageMsg.Image; // put up the processing image
}
else if (SS.I.AsyncImageRetrieval) // start async image retrieval
{
FormatImageFieldCalls++;
GetImageBitmapAsync(ci, dr, e.ListSourceRowIndex, fieldValue, imageMx, callId);
ffi.FormattedBitmap = (Bitmap)RetrievingImageMsg.Image; // put up the processing image
}
else // do synchronous image retrieval
{
GetImageBitmap(ci, dr, e.ListSourceRowIndex, fieldValue, imageMx, callId);
ffi.FormattedBitmap = imageMx.FormattedBitmap;
formatted = true;
}
}
}
//if (ci.Mc.DataType == MetaColumnType.CompoundId && String.IsNullOrEmpty(fmtdFld.Hyperlink)) ci = ci; // debug
//if (mdt is CompoundId) mdt = mdt; // debug
if (e.Column.ColumnEdit is RepositoryItemPictureEdit)
{
if (ffi != null && ffi.FormattedBitmap != null)
{
e.Value = ffi.FormattedBitmap;
}
else
{
e.Value = new Bitmap(1, 1); // avoid no-image data message
}
//ffi.FormattedBitmap.Save(@"c:\download\test.bmp"); // debug
}
else
{
e.Value = ffi.FormattedText; // non-picture column
}
if (ci.DataRowIndex == DataTable.Rows.Count - 1 && // if at end of DataTable && more rows available, request them
!Dtm.RowRetrievalComplete)
{
//Progress.Show("Retrieving data..."); // put up progress dialog if not already up
//if (WaitForMoreDataStartTime.Equals(DateTime.MinValue)) // say we've started waiting for data
//{
// WaitForMoreDataStartTime = DateTime.Now;
// ClientLog.Message("Set WaitForMoreDataStartTime: " + WaitForMoreDataStartTime.ToLongTimeString());
//}
if (Dtm.RowRetrievalState == RowRetrievalState.Paused)
{
Dtm.StartRowRetrieval(); // .ReadNextRowsFromQueryEngine(); // restart retrieval
}
}
else if (Lex.StartsWith(Progress.GetCaption(), "Retrieving data...") || Lex.IsUndefined(Progress.GetCaption()))
{ // hide any "Retrieving data..." message
Progress.Hide();
//SystemUtil.Beep();
}
Grid.LastRowRendered = e.ListSourceRowIndex;
if (DebugDetails)
{
debugMsg =
"Grid.GetData: " + callId + ", e.Row = " + e.ListSourceRowIndex +
", e.Col = " + e.Column.AbsoluteIndex + ", Formatted = " + (formatted ? "T" : "F") + ", Time(ms) = " + TimeOfDay.Delta(t0) +
", ColLabel = " + ci.Qc.ActiveLabel;
debugMsg += ", FieldValue = ";
if (fieldValue != null)
{
debugMsg += fieldValue.ToString();
}
debugMsg += ", e.Value = ";
if (e.Value != null)
{
debugMsg += e.Value.ToString();
}
else
{
debugMsg += "null";
}
ClientLog.Message(debugMsg);
}
// TODO: This does a some unnecessary hides which cause flashing of the window frame
// This happens when we are not at the end of the DataTable but don't know if any additional requests
// for rendering will occur. May be better to move this to DataTableManger when we detect
// that we have retrieved a row that is below the level of those displayed in the grid or all rows have been retrieved.
// Also maybe in MoleculeGridControl.RetrievalMonitorTimer_Tick
}
catch (Exception ex)
{
if (e.Column.ColumnEdit is RepositoryItemPictureEdit)
{
e.Value = new Bitmap(1, 1); // avoid no-image data message
}
else
{
e.Value = ex.Message;
}
string msg = "ColumnView_CustomUnboundColumnData Exception";
if (ci.Rfld != null)
{
msg += ", MetaColumn: " + ci.Rfld.MetaColumn.MetaTable.Name + "." + ci.Rfld.MetaColumn.Name;
}
msg += ", DataColIndex: " + ci.DataColIndex + ", DataRowIndex: " + ci.DataRowIndex;
if (fieldValue != null)
{
msg += ", Value: " + fieldValue.ToString();
}
ClientLog.Message(msg);
}
// t0 = TimeOfDay.Milliseconds() - t0;
// ClientLog.Message("CustomUnboundColumnData event time: " + t0);
}
/// <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
}