/// <inheritdoc/>
public IRenderingElement Generate(IReaction reaction, RendererModel model)
{
if (!model.GetShowReactionBoxes())
{
return(null);
}
if (reaction.Reactants.Count == 0)
{
return(new ElementGroup());
}
double separation = model.GetBondLength() / model.GetScale() / 2;
var totalBounds = BoundsCalculator.CalculateBounds(reaction.Reactants);
ElementGroup diagram = new ElementGroup();
double minX = totalBounds.Left;
double minY = totalBounds.Top;
double maxX = totalBounds.Right;
double maxY = totalBounds.Bottom;
var foregroundColor = model.GetForegroundColor();
diagram.Add(new RectangleElement(new Rect(minX - separation, minY - separation, maxX + separation, maxY + separation), foregroundColor));
diagram.Add(new TextElement(new Point((minX + maxX) / 2, minY - separation), "Reactants", foregroundColor));
return(diagram);
}
/// <inheritdoc/>
public IRenderingElement Generate(IReaction reaction, RendererModel model)
{
if (!model.GetShowReactionBoxes())
{
return(null);
}
var separation = model.GetBondLength() / model.GetScale();
var totalBounds = BoundsCalculator.CalculateBounds(reaction);
if (totalBounds.IsEmpty)
{
return(null);
}
var diagram = new ElementGroup();
var foregroundColor = model.GetForegroundColor();
diagram.Add(new RectangleElement(new Rect(totalBounds.Left - separation, totalBounds.Top - separation,
totalBounds.Right + separation, totalBounds.Bottom + separation),
foregroundColor));
if (reaction.Id != null)
{
diagram.Add(new TextElement(new Point((totalBounds.Left + totalBounds.Right) / 2, totalBounds.Top - separation),
reaction.Id, foregroundColor));
}
return(diagram);
}
private StandardSgroupGenerator(RendererModel parameters, StandardAtomGenerator atomGenerator, double stroke, Typeface font, double emSize, Color foreground)
{
this.font = font;
this.emSize = emSize;
this.scale = parameters.GetScale();
this.stroke = stroke;
double length = parameters.GetBondLength() / scale;
this.bracketDepth = parameters.GetSgroupBracketDepth() * length;
this.labelScale = parameters.GetSgroupFontScale();
// foreground is based on the carbon color
this.foreground = foreground;
this.atomGenerator = atomGenerator;
this.parameters = parameters;
}
/// <inheritdoc/>
public IRenderingElement Generate(IReaction reaction, RendererModel model)
{
if (!model.GetShowReactionBoxes())
{
return(null);
}
if (reaction.Products.Count == 0)
{
return(new ElementGroup());
}
double distance = model.GetBondLength() / model.GetScale() / 2;
Rect? totalBounds = null;
foreach (var molecule in reaction.Products)
{
var bounds = BoundsCalculator.CalculateBounds(molecule);
if (totalBounds == null)
{
totalBounds = bounds;
}
else
{
totalBounds = Rect.Union(totalBounds.Value, bounds);
}
}
if (totalBounds == null)
{
return(null);
}
ElementGroup diagram = new ElementGroup();
var foregroundColor = model.GetForegroundColor();
diagram.Add(new RectangleElement(
new Rect(
totalBounds.Value.Left - distance,
totalBounds.Value.Top - distance,
totalBounds.Value.Right + distance,
totalBounds.Value.Bottom + distance),
foregroundColor));
diagram.Add(new TextElement(
new Point(
(totalBounds.Value.Left + totalBounds.Value.Right) / 2,
totalBounds.Value.Top - distance),
"Products", foregroundColor));
return(diagram);
}
/// <inheritdoc/>
public IRenderingElement Generate(IReaction reaction, RendererModel model)
{
var totalBoundsReactants = BoundsCalculator.CalculateBounds(reaction.Reactants);
var totalBoundsProducts = BoundsCalculator.CalculateBounds(reaction.Products);
if (totalBoundsReactants == null || totalBoundsProducts == null)
{
return(null);
}
double separation = model.GetBondLength() / model.GetScale();
var foregroundColor = model.GetForegroundColor();
return(new ArrowElement(
new WPF::Point(totalBoundsReactants.Right + separation, totalBoundsReactants.CenterY()),
new WPF::Point(totalBoundsProducts.Left - separation, totalBoundsReactants.CenterY()),
1 / model.GetScale(), true, foregroundColor));
}
/// <summary>
/// Generate the intermediate <see cref="AtomSymbol"/> instances.
/// </summary>
/// <param name="container">structure representation</param>
/// <param name="symbolRemap">use alternate symbols (used for Sgroup shortcuts)</param>
/// <param name="visibility">defines whether an atom symbol is displayed</param>
/// <param name="parameters">render model parameters</param>
/// <returns>generated atom symbols (can contain <see langword="null"/>)</returns>
private AtomSymbol[] GenerateAtomSymbols(IAtomContainer container,
Dictionary <IAtom, string> symbolRemap,
SymbolVisibility visibility,
RendererModel parameters,
ElementGroup annotations,
Color foreground,
double stroke,
StandardDonutGenerator donutGen)
{
var scale = parameters.GetScale();
var annDist = parameters.GetAnnotationDistance() * (parameters.GetBondLength() / scale);
var annScale = (1 / scale) * parameters.GetAnnotationFontScale();
var annColor = parameters.GetAnnotationColor();
var halfStroke = stroke / 2;
var symbols = new AtomSymbol[container.Atoms.Count];
var builder = container.Builder;
// check if we should annotate attachment point numbers (maxAttach>1)
// and queue them all up for processing
var attachPoints = new List <IPseudoAtom>();
int maxAttach = 0;
for (int i = 0; i < container.Atoms.Count; i++)
{
var atom = container.Atoms[i];
if (IsHiddenFully(atom))
{
continue;
}
if (atom is IPseudoAtom)
{
var attachNum = ((IPseudoAtom)atom).AttachPointNum;
if (attachNum > 0)
{
attachPoints.Add((IPseudoAtom)atom);
}
if (attachNum > maxAttach)
{
maxAttach = attachNum;
}
}
var remapped = symbolRemap.ContainsKey(atom);
var bonds = container.GetConnectedBonds(atom);
var neighbors = container.GetConnectedAtoms(atom);
var visNeighbors = new List <IAtom>();
// if a symbol is remapped we only want to consider
// visible neighbors in the alignment calculation, otherwise
// we include all neighbors
foreach (var neighbor in neighbors)
{
if (!remapped || !IsHidden(neighbor))
{
visNeighbors.Add(neighbor);
}
}
var auxVectors = new List <Vector2>(1);
// only generate if the symbol is visible
if (visibility.Visible(atom, bonds, parameters) || remapped)
{
var hPosition = HydrogenPositionTools.Position(atom, visNeighbors);
if (atom.ImplicitHydrogenCount != null && atom.ImplicitHydrogenCount > 0)
{
auxVectors.Add(hPosition.Vector());
}
if (remapped)
{
symbols[i] = atomGenerator.GenerateAbbreviatedSymbol(symbolRemap[atom], hPosition);
}
else if (donutGen.IsChargeDelocalised(atom))
{
var charge = atom.FormalCharge;
atom.FormalCharge = 0;
// can't think of a better way to handle this without API
// change to symbol visibility
if (atom.AtomicNumber != 6)
{
symbols[i] = atomGenerator.GenerateSymbol(container, atom, hPosition, parameters);
}
atom.FormalCharge = charge;
}
else
{
symbols[i] = atomGenerator.GenerateSymbol(container, atom, hPosition, parameters);
}
if (symbols[i] != null)
{
// defines how the element is aligned on the atom point, when
// aligned to the left, the first character 'e.g. Cl' is used.
if (visNeighbors.Count < 4)
{
if (hPosition == HydrogenPosition.Left)
{
symbols[i] = symbols[i].AlignTo(AtomSymbol.SymbolAlignment.Right);
}
else
{
symbols[i] = symbols[i].AlignTo(AtomSymbol.SymbolAlignment.Left);
}
}
var p = atom.Point2D;
if (p == null)
{
throw new ArgumentException("Atom did not have 2D coordinates");
}
symbols[i] = symbols[i].Resize(1 / scale, 1 / -scale).Center(p.Value.X, p.Value.Y);
}
}
var label = GetAnnotationLabel(atom);
if (label != null)
{
// to ensure consistent draw distance we need to adjust the annotation distance
// depending on whether we are drawing next to an atom symbol or not.
double strokeAdjust = symbols[i] != null ? -halfStroke : 0;
var vector = NewAtomAnnotationVector(atom, bonds, auxVectors);
var annOutline = GenerateAnnotation(atom.Point2D.Value, label, vector, annDist + strokeAdjust, annScale, font, emSize, symbols[i]);
// the AtomSymbol may migrate during bond generation and therefore the annotation
// needs to be tied to the symbol. If no symbol is available the annotation is
// fixed and we can add it to the annotation ElementGroup right away.
if (symbols[i] != null)
{
symbols[i] = symbols[i].AddAnnotation(annOutline);
}
else
{
annotations.Add(GeneralPath.ShapeOf(annOutline.GetOutline(), annColor));
}
}
}
// label attachment points
if (maxAttach > 1)
{
var attachNumOutlines = new List <TextOutline>();
double maxRadius = 0;
foreach (IPseudoAtom atom in attachPoints)
{
int attachNum = atom.AttachPointNum;
// to ensure consistent draw distance we need to adjust the annotation distance
// depending on whether we are drawing next to an atom symbol or not.
var strokeAdjust = -halfStroke;
var vector = NewAttachPointAnnotationVector(
atom,
container.GetConnectedBonds(atom),
new List <Vector2>());
var outline = GenerateAnnotation(atom.Point2D.Value,
attachNum.ToString(),
vector,
1.75 * annDist + strokeAdjust,
annScale,
new Typeface(font.FontFamily, font.Style, WPF.FontWeights.Bold, font.Stretch),
emSize,
null);
attachNumOutlines.Add(outline);
var w = outline.GetBounds().Width;
var h = outline.GetBounds().Height;
var r = Math.Sqrt(w * w + h * h) / 2;
if (r > maxRadius)
{
maxRadius = r;
}
}
foreach (var outline in attachNumOutlines)
{
var group = new ElementGroup();
var radius = 2 * stroke + maxRadius;
var shape = new EllipseGeometry(outline.GetCenter(), radius, radius);
var area1 = Geometry.Combine(shape, outline.GetOutline(), GeometryCombineMode.Exclude, Transform.Identity);
group.Add(GeneralPath.ShapeOf(area1, foreground));
annotations.Add(group);
}
}
return(symbols);
}
/// <summary>
/// Utility method for recalling a depiction in pixels to one in millimeters.
/// </summary>
/// <param name="bondLength">the desired bond length (mm)</param>
/// <returns>the scaling factor</returns>
internal double RescaleForBondLength(double bondLength)
{
return(bondLength / model.GetBondLength());
}
