/// <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);
}
/// <inheritdoc/>
public IRenderingElement Generate(IAtomContainer container, RendererModel parameters)
{
if (container.Atoms.Count == 0)
{
return(new ElementGroup());
}
var symbolRemap = new Dictionary <IAtom, string>();
StandardSgroupGenerator.PrepareDisplayShortcuts(container, symbolRemap);
var scale = parameters.GetScale();
var visibility = parameters.GetVisibility();
var coloring = parameters.GetAtomColorer();
var annotationColor = parameters.GetAnnotationColor();
var foreground = coloring.GetAtomColor(container.Builder.NewAtom("C"));
// the stroke width is based on the font. a better method is needed to get
// the exact font stroke but for now we use the width of the pipe character.
var fontStroke = new TextOutline("|", font, emSize).Resize(1 / scale, 1 / scale).GetBounds().Width;
var stroke = parameters.GetStrokeRatio() * fontStroke;
var annotations = new ElementGroup();
var donutGenerator = new StandardDonutGenerator(container, font, emSize, parameters, stroke);
var donuts = donutGenerator.Generate();
var symbols = GenerateAtomSymbols(container, symbolRemap,
visibility, parameters,
annotations, foreground,
stroke, donutGenerator);
var bondElements = StandardBondGenerator.GenerateBonds(container, symbols,
parameters, stroke,
font, emSize, annotations,
donutGenerator);
var style = parameters.GetHighlighting();
var glowWidth = parameters.GetOuterGlowWidth();
var backLayer = new ElementGroup();
var middleLayer = new ElementGroup();
var frontLayer = new ElementGroup();
// bond elements can simply be added to the element group
for (int i = 0; i < container.Bonds.Count; i++)
{
var bond = container.Bonds[i];
if (IsHidden(bond))
{
continue;
}
var highlight = GetHighlightColor(bond, parameters);
if (highlight != null && style == HighlightStyle.OuterGlow)
{
backLayer.Add(MarkedElement.Markup(OuterGlow(bondElements[i], highlight.Value, glowWidth, stroke), "outerglow"));
}
if (highlight != null && style == HighlightStyle.Colored)
{
frontLayer.Add(MarkedElement.MarkupBond(Recolor(bondElements[i], highlight.Value), bond));
}
else
{
middleLayer.Add(MarkedElement.MarkupBond(bondElements[i], bond));
}
}
// bonds for delocalised aromatic
frontLayer.Add(donuts);
// convert the atom symbols to IRenderingElements
for (int i = 0; i < container.Atoms.Count; i++)
{
var atom = container.Atoms[i];
if (IsHidden(atom))
{
continue;
}
var highlight = GetHighlightColor(atom, parameters);
var color = GetColorOfAtom(symbolRemap, coloring, foreground, style, atom, highlight);
if (symbols[i] == null)
{
// we add a 'ball' around atoms with no symbols (e.g. carbons)
if (highlight != null && style == HighlightStyle.OuterGlow)
{
backLayer.Add(MarkedElement.Markup(new OvalElement(ToPoint(atom.Point2D.Value), 1.75 * glowWidth * stroke, true, highlight.Value), "outerglow"));
}
continue;
}
var symbolElements = new ElementGroup();
foreach (var shape in symbols[i].GetOutlines())
{
GeneralPath path = GeneralPath.ShapeOf(shape, color);
symbolElements.Add(path);
}
// add the annotations of the symbol to the annotations ElementGroup
foreach (var shape in symbols[i].GetAnnotationOutlines())
{
annotations.Add(MarkedElement.Markup(GeneralPath.ShapeOf(shape, annotationColor), "annotation"));
}
if (highlight != null && style == HighlightStyle.OuterGlow)
{
backLayer.Add(MarkedElement.Markup(OuterGlow(symbolElements, highlight.Value, glowWidth, stroke), "outerglow"));
}
if (highlight != null && style == HighlightStyle.Colored)
{
frontLayer.Add(MarkedElement.MarkupAtom(symbolElements, atom));
}
else
{
middleLayer.Add(MarkedElement.MarkupAtom(symbolElements, atom));
}
}
// Add the Sgroups display elements to the front layer
var sgroups = StandardSgroupGenerator.Generate(parameters, stroke, font, emSize, foreground, atomGenerator, symbols, container);
frontLayer.Add(sgroups);
// Annotations are added to the front layer.
frontLayer.Add(annotations);
var group = new ElementGroup
{
backLayer,
middleLayer,
frontLayer
};
return(MarkedElement.MarkupMol(group, container));
}