private static void AppendAllOoXml(A.GraphicData graphicData, Wpg.WordprocessingGroup wordprocessingGroup, A.Graphic graphic,
Wp.Inline inline, Drawing drawing, Run run)
{
graphicData.Append(wordprocessingGroup);
graphic.Append(graphicData);
inline.Append(graphic);
drawing.Append(inline);
run.Append(drawing);
}
public Run GenerateRun()
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
_telemetry.Write(module, "Verbose", "Called");
//start off progress monitoring
Progress pb = new Progress();
pb.TopLeft = _topLeft;
//lists of objects for drawing
_atomLabelCharacters = new List <AtomLabelCharacter>();
_bondLines = new List <BondLine>();
Stopwatch swr = new Stopwatch();
Stopwatch sw = new Stopwatch();
//Create a run
Run run = new Run();
sw.Start();
swr.Start();
//set the median bond length
_medianBondLength = GeometryTool.GetMedianBondLength2D(_chemistryModel.AllBonds);
int moleculeNo = 0;
foreach (Molecule mol in _chemistryModel.Molecules)
{
moleculeNo++;
// Step 1- gather the atom information together
Debug.WriteLine($"{module} Starting Step 1");
//_telemetry.Write(module, "Verbose", $"Starting Step 1 for molecule {moleculeNo}");
ProcessAtoms(mol, pb, moleculeNo, _pt);
Debug.WriteLine("Elapsed time " + sw.ElapsedMilliseconds.ToString("##,##0") + "ms");
//_telemetry.Write(module, "Timing", $"Step 1 for molecule {moleculeNo} took " + sw.ElapsedMilliseconds.ToString("#,##0", CultureInfo.InvariantCulture) + "ms");
sw.Reset();
sw.Start();
// Step 2- gather the bond information together
Debug.WriteLine($"{module} Starting Step 2");
//_telemetry.Write(module, "Verbose", $"Starting Step 2 for molecule {moleculeNo}");
ProcessBonds(mol, pb, moleculeNo);
Debug.WriteLine("Elapsed time " + sw.ElapsedMilliseconds.ToString("##,##0") + "ms");
//_telemetry.Write(module, "Timing", $"Step 2 for molecule {moleculeNo} took " + sw.ElapsedMilliseconds.ToString("#,##0", CultureInfo.InvariantCulture) + "ms");
sw.Reset();
sw.Start();
if (_options.ShowRingCentres)
{
// Save Rings for later
foreach (Ring ring in mol.Rings)
{
_rings.Add(ring.UniqueID, ring);
}
}
}
Debug.WriteLine($"{module} Starting Step 3");
//_telemetry.Write(module, "Verbose", "Starting Step 3");
IncreaseCanvasSize();
Debug.WriteLine("Elapsed time " + sw.ElapsedMilliseconds.ToString("##,##0") + "ms");
//_telemetry.Write(module, "Timing", "Step 3 took " + sw.ElapsedMilliseconds.ToString("#,##0", CultureInfo.InvariantCulture) + "ms");
sw.Reset();
sw.Start();
if (_options.ClipLines)
{
Debug.WriteLine($"{module} Starting Step 4");
//_telemetry.Write(module, "Verbose", "Starting Step 4");
#region Step 4 - Shrink bond lines
ShrinkBondLinesPass1(pb);
ShrinkBondLinesPass2(pb);
#endregion Step 4 - Shrink bond lines
Debug.WriteLine("Elapsed time " + sw.ElapsedMilliseconds.ToString("##,##0") + "ms");
//_telemetry.Write(module, "Timing", "Step 4 took " + sw.ElapsedMilliseconds.ToString("#,##0", CultureInfo.InvariantCulture) + "ms");
sw.Reset();
sw.Start();
}
Debug.WriteLine($"{module} Starting Step 5");
//_telemetry.Write(module, "Verbose", "Starting Step 5");
#region Step 5 - Create main OoXml drawing objects
Drawing drawing1 = new Drawing();
A.Graphic graphic1 = CreateGraphic();
A.GraphicData graphicData1 = CreateGraphicData();
Wpg.WordprocessingGroup wordprocessingGroup1 = new Wpg.WordprocessingGroup();
// Create Inline Drawing using canvas extents
Wp.Inline inline1 = CreateInline(graphicData1, wordprocessingGroup1);
#endregion Step 5 - Create main OoXml drawing objects
Debug.WriteLine("Elapsed time " + sw.ElapsedMilliseconds.ToString("##,##0") + "ms");
//_telemetry.Write(module, "Timing", "Step 5 took " + sw.ElapsedMilliseconds.ToString("#,##0", CultureInfo.InvariantCulture) + "ms");
sw.Reset();
sw.Start();
#region Step 5a - Diagnostics
if (_options.ShowMoleculeBoundingBoxes)
{
DrawBox(wordprocessingGroup1, _modelExtents, "00ff00", 1);
foreach (Molecule mol in _chemistryModel.Molecules)
{
DrawBox(wordprocessingGroup1, mol.BoundingBox, "0000ff", 1);
DrawBox(wordprocessingGroup1, MoleculeExtents(mol), "ff0000", 1);
}
DrawBox(wordprocessingGroup1, _canvasExtents, "000000", 1);
}
if (_options.ShowRingCentres)
{
ShowRingCentres(wordprocessingGroup1);
}
if (_options.ShowAtomPositions)
{
ShowAtomCentres(wordprocessingGroup1);
}
if (_options.ShowHulls)
{
ShowConvexHulls(wordprocessingGroup1);
}
#endregion Step 5a - Diagnostics
Debug.WriteLine($"{module} Starting Step 6");
//_telemetry.Write(module, "Verbose", "Starting Step 6");
#region Step 6 - Create and append OoXml objects for all Bond Lines
AppendBondOoxml(pb, wordprocessingGroup1);
#endregion Step 6 - Create and append OoXml objects for all Bond Lines
Debug.WriteLine("Elapsed time " + sw.ElapsedMilliseconds.ToString("##,##0") + "ms");
//_telemetry.Write(module, "Timing", "Step 6 took " + sw.ElapsedMilliseconds.ToString("#,##0", CultureInfo.InvariantCulture) + "ms");
sw.Reset();
sw.Start();
Debug.WriteLine($"{module} Starting Step 7");
//_telemetry.Write(module, "Verbose", "Starting Step 7");
#region Step 7 - Create and append OoXml objects for Atom Labels
AppendAtomLabelOoxml(pb, wordprocessingGroup1);
#endregion Step 7 - Create and append OoXml objects for Atom Labels
Debug.WriteLine("Elapsed time " + sw.ElapsedMilliseconds.ToString("##,##0") + "ms");
//_telemetry.Write(module, "Timing", "Step 7 took " + sw.ElapsedMilliseconds.ToString("#,##0", CultureInfo.InvariantCulture) + "ms");
sw.Reset();
sw.Start();
Debug.WriteLine($"{module} Starting Step 8");
//_telemetry.Write(module, "Verbose", "Starting Step 8");
#region Step 8 - Append OoXml drawing objects to OoXml run object
AppendAllOoXml(graphicData1, wordprocessingGroup1, graphic1, inline1, drawing1, run);
#endregion Step 8 - Append OoXml drawing objects to OoXml run object
Debug.WriteLine("Elapsed time " + sw.ElapsedMilliseconds.ToString("##,##0") + "ms");
//_telemetry.Write(module, "Timing", "Step 8 took " + sw.ElapsedMilliseconds.ToString("#,##0", CultureInfo.InvariantCulture) + "ms");
sw.Reset();
sw.Start();
double abl = _chemistryModel.MeanBondLength;
Debug.WriteLine("Elapsed time for GenerateRun " + swr.ElapsedMilliseconds.ToString("#,##0", CultureInfo.InvariantCulture) + "ms");
_telemetry.Write(module, "Timing", $"Rendering {_chemistryModel.Molecules.Count} molecules with {_chemistryModel.AllAtoms.Count} atoms and {_chemistryModel.AllBonds.Count} bonds took {swr.ElapsedMilliseconds.ToString("##,##0")} ms; Average Bond Length: {abl.ToString("#0.00")}");
ShutDownProgress(pb);
return(run);
}
