/// <summary>
/// Convert this molecule to a new type
/// </summary>
/// <param name="newType"></param>
public void ConvertToNewType(
MoleculeFormat newType)
{
if (PrimaryFormat == newType)
{
return; // no change in type
}
else if (PrimaryFormat == MoleculeFormat.Molfile && newType == MoleculeFormat.Chime)
{
if (!Lex.IsNullOrEmpty(MolfileString))
{
ChimeString = MolfileStringToChimeString(MolfileString);
}
PrimaryFormat = MoleculeFormat.Chime;
}
else if (PrimaryFormat == MoleculeFormat.Chime && newType == MoleculeFormat.Molfile)
{
if (!Lex.IsNullOrEmpty(ChimeString))
{
MolfileString = ChimeStringToMolfileString(ChimeString);
}
PrimaryFormat = MoleculeFormat.Molfile;
}
else
{
MoleculeMx cs2 = ConvertTo(newType);
cs2.MemberwiseCopy(this);
}
return;
}
/// <summary>
/// Set molecule value including the associated native CDK IAtomContainer
/// </summary>
/// <param name="molFormat"></param>
/// <param name="molString"></param>
public void SetMolecule(
MoleculeFormat molFormat,
string molString)
{
if (molFormat == _molFormat && Lex.Eq(molString, _molString))
{
return; // no change
}
if (molFormat == MoleculeFormat.Molfile)
{
NativeMol = MolfileToAtomContainer(molString);
}
else if (molFormat == MoleculeFormat.Chime)
{
string molfile = MoleculeMx.ChimeStringToMolfileString(molString);
NativeMol = MolfileToAtomContainer(molfile);
}
else if (molFormat == MoleculeFormat.Smiles)
{
NativeMol = SmilesToAtomContainer(molString);
}
else if (molFormat == MoleculeFormat.Unknown)
{
NativeMol = null;
}
_molFormat = molFormat;
_molString = molString;
}
/// <summary>
/// Get molecule
/// </summary>
/// <param name="molFormat"></param>
/// <param name="molString"></param>
public void GetMolecule(
out MoleculeFormat molFormat,
out string molString)
{
molFormat = _molFormat;
molString = _molString;
}
/// <summary>
/// Convert from one format to another
/// </summary>
/// <param name="newFormat"></param>
/// <returns></returns>
public MoleculeMx ConvertTo(
MoleculeFormat molFormatType)
{
string molString, msg;
bool conversionFailed = false;
MoleculeMx mol = new MoleculeMx(molFormatType);
try
{
// If no change in type, just copy value
if (this.PrimaryFormat == molFormatType) // any change in type?
{
molString = this.PrimaryValue;
}
else
{
molString = GetMoleculeString(molFormatType); // convert from old type if possible
}
mol.SetPrimaryTypeAndValue(molFormatType, molString);
return(mol);
}
catch (Exception ex) // handle structures that don't convert - issue #216
{
//DebugLog.Message("ChemicalStructure.Convert exception for structure: \r\n" + Value + "\r\n" +
// DebugLog.FormatExceptionMessage(ex));
//throw new Exception(ex.Message, ex);
return(new MoleculeMx(PrimaryFormat, "")); // return blank structure
}
}
/// <summary>
/// Get the molecule string of the specified type
/// Do a conversion from an existing type if specified type not yet detined for the molecule
/// </summary>
/// <param name="newType"></param>
/// <returns></returns>
public string GetMoleculeString(
MoleculeFormat newType)
{
try
{
switch (newType)
{
case MoleculeFormat.Molfile:
return(GetMolfileString());
case MoleculeFormat.Chime:
return(GetChimeString());
case MoleculeFormat.Smiles:
return(GetSmilesString());
case MoleculeFormat.Helm:
return(GetHelmString());
case MoleculeFormat.Sequence:
return(GetSequenceString());
case MoleculeFormat.Fasta:
return(GetFastaString());
default: throw new Exception("Can't convert type: " + this.PrimaryFormat);
}
}
catch (Exception ex) // handle structures that don't convert - issue #216
{
throw new Exception(ex.Message, ex);
}
}
/// <summary>
/// SetMoleculeAndRender
/// </summary>
/// <param name="format"></param>
/// <param name="value"></param>
public void SetMoleculeAndRender(MoleculeFormat format, string value)
{
MolFormat = format;
MolString = value;
CdkMol = new CdkMol(MolFormat, MolString);
RenderMolecule();
return;
}
/// <summary>
/// Construct from mol format and string
/// </summary>
public CdkMol(
MoleculeFormat molFormat,
string molString)
{
if (Lex.IsUndefined(molString))
{
return; // create new structure
}
SetMolecule(molFormat, molString);
return;
}
/// <summary>
/// Execute structure search for structures stored in an general Oracle table text column
/// </summary>
void ExecuteInternalOracleStructureColumnSearch()
{
SelectList = new List <MetaColumn>();
QueryColumn scQc = null;
MoleculeFormat structureFormat = MoleculeFormat.Unknown;
MetaColumn keyMc = Eqp.QueryTable.MetaTable.KeyMetaColumn;
MetaColumn strMc = null;
foreach (QueryColumn qc2 in Eqp.QueryTable.QueryColumns)
{
if (qc2.Selected || qc2.SortOrder != 0)
{
SelectList.Add(qc2.MetaColumn);
}
if (qc2.Criteria == "")
{
continue;
}
if (qc2.MetaColumn.DataType == MetaColumnType.Structure)
{
strMc = qc2.MetaColumn;
if (Lex.Eq(strMc.DataTransform, "FromMolFile"))
{
structureFormat = MoleculeFormat.Molfile;
}
else if (Lex.Eq(strMc.DataTransform, "FromChime"))
{
structureFormat = MoleculeFormat.Chime;
}
else if (Lex.Eq(strMc.DataTransform, "FromSmiles"))
{
structureFormat = MoleculeFormat.Smiles;
}
break;
}
else
{
} // allow criteria on other cols?
}
if (strMc == null)
{
throw new Exception("Structure criteria not found");
}
string sql =
"select " + keyMc.Name + ", " + strMc.Name + " " +
"from " + Eqp.QueryTable.MetaTable.TableMap;
ExecuteInternalOracleStructureColumnSearch(sql, structureFormat);
return;
}
/// <summary>
/// Try to get molfile form of molecule doing a conversion from another format as necessary
/// </summary>
/// <param name="molFormat"></param>
/// <param name="molString"></param>
/// <returns></returns>
public bool TryGetMoleculeString(
MoleculeFormat molFormat,
out string molString)
{
try
{
molString = GetMoleculeString(molFormat);
return(true);
}
catch (Exception ex)
{
molString = null;
return(false);
}
}
/// <summary>
/// Convert any ChemicalStructures containing a sketch value to a ChimeString for proper serialization
/// </summary>
/// <param name="oa"></param>
public static void ConvertMoleculesToChimeStrings(object[] oa)
{
for (int ci = 0; ci < oa.Length; ci++)
{
if (!(oa[ci] is MoleculeMx))
{
continue;
}
MoleculeMx cs = oa[ci] as MoleculeMx;
if (Math.Abs(1) == 1)
{
continue; // noop for now
}
//if (cs.Type != StructureFormat.Sketch) continue; // obsolete
MoleculeFormat type = MoleculeFormat.Chime;
string value = cs.GetChimeString();
cs.SetPrimaryTypeAndValue(type, value);
}
}
/// <summary>
/// Execute structure search for structures stored in an Oracle text column
/// </summary>
/// <param name="sql">Basic sql to select key & structure</param>
public void ExecuteInternalOracleStructureColumnSearch(
string sql,
MoleculeFormat structureFormat)
{
string cid, molString;
object[] vo;
MoleculeMx cs;
bool match = false;
QueryColumn molsimQc = Eqp.QueryTable.GetSelectedMolsimQueryColumn(); // get any column to return similarity score in
DbCommandMx drd = new DbCommandMx();
if (Eqp.SearchKeySubset == null)
{
drd.Prepare(sql);
drd.ExecuteReader();
}
else // limit to list
{
sql += " where " + Eqp.QueryTable.MetaTable.KeyMetaColumn.Name + " in (<list>)";
drd.PrepareListReader(sql, DbType.String);
List <string> dbKeySubset = new List <string>();
foreach (string key in Eqp.SearchKeySubset)
{
string dbKey = CompoundId.NormalizeForDatabase(key, Eqp.QueryTable.MetaTable);
dbKeySubset.Add(dbKey);
}
drd.ExecuteListReader(dbKeySubset);
}
drd.CheckForCancel = Eqp.CheckForCancel; // set cancel check flag
StructureMatcher matcher = new StructureMatcher(); // allocate structure matcher
List <object[]> results = new List <object[]>();
int matchCount = 0;
while (drd.Read())
{
cid = drd.GetObject(0).ToString();
cid = CompoundId.Normalize(cid, Eqp.QueryTable.MetaTable); // normalize adding prefix as needed
molString = drd.GetString(1);
if (String.IsNullOrEmpty(molString))
{
continue;
}
cs = new MoleculeMx(structureFormat, molString);
if (Pssc.SearchType == StructureSearchType.Substructure)
{
if (matcher.IsSSSMatch(Pssc.Molecule, cs))
{
vo = new object[SelectList.Count];
vo[0] = CompoundId.Normalize(cid, Eqp.QueryTable.MetaTable); // normalize adding prefix
results.Add(vo);
}
}
else if (Pssc.SearchType == StructureSearchType.MolSim)
{
double score = matcher.Molsim(Pssc.Molecule, cs, Pssc.SimilarityType);
if (score >= Pssc.MinimumSimilarity)
{
vo = new object[SelectList.Count];
vo[0] = CompoundId.Normalize(cid, Eqp.QueryTable.MetaTable); // normalize adding prefix
if (vo.Length >= 2)
{
vo[1] = (float)score;
}
results.Add(vo);
}
}
else if (Pssc.SearchType == StructureSearchType.FullStructure)
{
if (matcher.FullStructureMatch(Pssc.Molecule, cs, Pssc.Options))
{
vo = new object[SelectList.Count];
vo[0] = CompoundId.Normalize(cid, Eqp.QueryTable.MetaTable); // normalize adding prefix
results.Add(vo);
}
}
matchCount++;
// if (matchCount >100) break; // debug
if (drd.Cancelled)
{
Eqp.Qe.Cancelled = true;
drd.Dispose();
Results = null;
return;
}
}
drd.Dispose();
Results = results;
return;
}
public void GetMolecule(out MoleculeFormat format, out string value)
{
format = MolFormat;
value = MolString;
return;
}
/// <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>
/// 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>
/// Construct from mol format and string
/// </summary>
/// <param name="molFormat"></param>
/// <param name="molString"></param>
/// <returns></returns>
public ICdkMol NewCdkMol(
MoleculeFormat molFormat,
string molString)
{
return(new CdkMol(molFormat, molString));
}
public static void Load()
{
string value;
int i1;
PrefDict = UserObjectDao.GetUserParameters(Security.UserName);
SS.I.PreferredProjectId = // get preferred project
Get("PreferredProject", "DEFAULT_FOLDER");
SS.I.TableColumnZoom = GetInt("TableColumnZoom", 100);
SS.I.GraphicsColumnZoom = GetInt("GraphicsColumnZoom", 100);
SS.I.ScrollGridByPixel = GetBool("ScrollGridByPixel", false); // default to row scrolling
SS.I.AsyncImageRetrieval = GetBool("AsyncImageRetrieval", true);
try // get preferred number format
{
value = Get("DefaultNumberFormat", "SigDigits");
EnumUtil.TryParse(value, out SS.I.DefaultNumberFormat);
SS.I.DefaultDecimals = GetInt("DefaultDecimals", 3);
}
catch (Exception ex) { }
SS.I.RepeatReport = // repeating report across page
GetBool("RepeatReport", false);
MqlUtil.DefaultToSingleStepQueryExecution = // default to single step query execution
GetBool("DefaultToSingleStepQueryExecution", false);
if (MqlUtil.DefaultToSingleStepQueryExecution)
{
QueryEngine.SetParameter("DefaultToSingleStepQueryExecution", MqlUtil.DefaultToSingleStepQueryExecution.ToString()); // set in QE for current session
}
SS.I.FindRelatedCpdsInQuickSearch =
GetBool("FindRelatedCpdsInQuickSearch", true);
SS.I.RestoreWindowsAtStartup = // get bool for restoring windows at startup
GetBool("RestoreWindowsAtStartup", false);
SS.I.BreakHtmlPopupsAtPageWidth =
GetBool("BreakHtmlPopupsAtPageWidth", true);
try // qualified number splitting
{
value = Get("QualifiedNumberSplit");
SS.I.QualifiedNumberSplit = QnfSplitControl.DeserializeQualifiedNumberSplit(value);
}
catch (Exception ex) { }
SS.I.HilightCidChanges =
GetBool("HilightCorpIdChanges", true);
SS.I.RemoveLeadingZerosFromCids =
GetBool("RemoveLeadingZerosFromCids", true);
SS.I.GridMarkCheckBoxesInitially = // (always false initially now)
GetBool("GridMarkCheckBoxesInitially", false);
value = Get("DefaultHorizontalAlignment", MetaColumn.SessionDefaultHAlignment.ToString());
MetaColumn.SessionDefaultHAlignment = (HorizontalAlignmentEx)Enum.Parse(typeof(HorizontalAlignmentEx), value, true);
value = Get("DefaultVerticalAlignment", MetaColumn.SessionDefaultVAlignment.ToString());
MetaColumn.SessionDefaultVAlignment = (VerticalAlignmentEx)Enum.Parse(typeof(VerticalAlignmentEx), value, true);
SS.I.EvenRowBackgroundColor =
Color.FromArgb(GetInt("EvenRowBackgroundColor", Color.WhiteSmoke.ToArgb())); // slightly contrasting color
SS.I.OddRowBackgroundColor =
Color.FromArgb(GetInt("OddRowBackgroundColor", Color.White.ToArgb()));
ClientDirs.DefaultMobiusUserDocumentsFolder = Preferences.Get("DefaultExportFolder", ClientDirs.DefaultMobiusUserDocumentsFolder);
MoleculeFormat molFormat = MoleculeFormat.Molfile;
value = Get("PreferredMoleculeFormat", "Molfile");
if (Enum.TryParse(value, out molFormat))
{
MoleculeMx.PreferredMoleculeFormat = molFormat;
}
return;
}
/// <summary>
/// Construct from mol format and string
/// </summary>
/// <param name="molFormat"></param>
/// <param name="molString"></param>
/// <returns></returns>
public INativeMolMx NewCdkMol(
MoleculeFormat molFormat,
string molString)
{
return(new CdkMol(molFormat, molString));
}
