private IRenderingElement GenerateAbbreviationSgroup(IAtomContainer mol, Sgroup sgroup)
{
string label = sgroup.Subscript;
// already handled by symbol remapping
if (sgroup.Bonds.Count > 0 || string.IsNullOrEmpty(label))
{
return(new ElementGroup());
}
if (!CheckAbbreviationHighlight(mol, sgroup))
{
return(new ElementGroup());
}
// we're showing a label where there were no atoms before, we put it in the
// middle of all of those which were hidden
var sgroupAtoms = sgroup.Atoms;
Debug.Assert(sgroupAtoms.Any());
var highlight = sgroupAtoms.First().GetProperty <Color>(StandardGenerator.HighlightColorKey);
var style = parameters.GetHighlighting();
var glowWidth = parameters.GetOuterGlowWidth();
Vector2 labelCoords = GeometryUtil.Get2DCenter(sgroupAtoms);
ElementGroup labelgroup = new ElementGroup();
foreach (var outline in atomGenerator.GenerateAbbreviatedSymbol(label, HydrogenPosition.Right)
.Resize(1 / scale, 1 / -scale)
.GetOutlines())
{
if (highlight != null && style == HighlightStyle.Colored)
{
labelgroup.Add(GeneralPath.ShapeOf(outline, highlight));
}
else
{
labelgroup.Add(GeneralPath.ShapeOf(outline, foreground));
}
}
if (highlight != null && style == HighlightStyle.OuterGlow)
{
ElementGroup group = new ElementGroup
{
// outer glow needs to be being the label
StandardGenerator.OuterGlow(labelgroup, highlight, glowWidth, stroke),
labelgroup
};
return(group);
}
else
{
return(MarkedElement.MarkupAtom(labelgroup, null));
}
}
/// <inheritdoc/>
public virtual IRenderingElement Generate(IAtomContainer container, RendererModel model)
{
ElementGroup elementGroup = new ElementGroup();
foreach (var atom in container.Atoms)
{
elementGroup.Add(MarkedElement.MarkupAtom(this.Generate(container, atom, model), atom));
}
return(elementGroup);
}
private Bounds GenerateReactionConditions(IReaction chemObj, Color fg, double scale)
{
var title = chemObj.GetProperty <string>(CDKPropertyName.ReactionConditions);
if (string.IsNullOrEmpty(title))
{
return(new Bounds());
}
return(new Bounds(MarkedElement.Markup(StandardGenerator.EmbedText(font, emSize, title, fg, 1 / scale), "conditions")));
}
/// <summary>
/// Generate a bound element that is the title of the provided molecule. If title
/// is not specified an empty bounds is returned.
/// </summary>
/// <param name="chemObj">molecule or reaction</param>
/// <returns>bound element</returns>
private Bounds GenerateTitle(RendererModel model, IChemObject chemObj, double scale)
{
var title = chemObj.GetProperty <string>(CDKPropertyName.Title);
if (string.IsNullOrEmpty(title))
{
return(new Bounds());
}
scale = 1 / scale * model.GetTitleFontScale();
return(new Bounds(MarkedElement.Markup(StandardGenerator.EmbedText(font, emSize, title, model.GetTitleColor(), scale), "title")));
}
public void MarkedElementTest()
{
SvgDrawVisitor visitor = new SvgDrawVisitor(50, 50, Depiction.UnitsMM);
visitor.Visit(MarkedElement.Markup(new LineElement(new WPF.Point(0, 0), new WPF.Point(1, 1), 0.5, Colors.Red), "test-class"));
Assert.AreEqual(
"<?xml version='1.0' encoding='UTF-8'?>\n"
+ "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\" \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n"
+ "<svg version='1.2' xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' width='50mm' height='50mm' viewBox='0 0 50 50'>\n"
+ " <desc>Generated by the Chemistry Development Kit (http://github.com/cdk)</desc>\n"
+ " <g stroke-linecap='round' stroke-linejoin='round'>\n"
+ " <line x1='0' y1='0' x2='1' y2='1' stroke='#FF0000' stroke-width='0.5'/>\n"
+ " </g>\n"
+ "</svg>\n",
visitor.ToString());
}
/// <inheritdoc/>
public virtual IRenderingElement Generate(IAtomContainer container, RendererModel model)
{
ElementGroup group = new ElementGroup();
this.ringSet = this.GetRingSet(container);
//Sort the ringSet consistently to ensure consistent rendering.
//If this is omitted, the bonds may 'tremble'.
ringSet.Sort(new AtomContainerComparatorBy2DCenter <IRing>());
foreach (var bond in container.Bonds)
{
var bondElement = this.Generate(bond, model);
if (bondElement != null)
{
group.Add(MarkedElement.MarkupBond(bondElement, bond));
}
}
return(group);
}
private IRenderingElement GenerateAbbreviationSgroup(IAtomContainer mol, Sgroup sgroup)
{
string label = sgroup.Subscript;
// already handled by symbol remapping
if (sgroup.Bonds.Count > 0 || string.IsNullOrEmpty(label))
{
return(new ElementGroup());
}
if (!CheckAbbreviationHighlight(mol, sgroup))
{
return(new ElementGroup());
}
// we're showing a label where there were no atoms before, we put it in the
// middle of all of those which were hidden
var sgroupAtoms = sgroup.Atoms;
Debug.Assert(sgroupAtoms.Any());
var highlight = sgroupAtoms.First().GetProperty <Color>(StandardGenerator.HighlightColorKey);
var style = parameters.GetHighlighting();
var glowWidth = parameters.GetOuterGlowWidth();
Vector2 labelLocation;
if (mol.Atoms.Count == sgroup.Atoms.Count)
{
labelLocation = GeometryUtil.Get2DCenter(sgroupAtoms);
}
else
{
// contraction of part of a fragment, e.g. SALT
// here we work out the point we want to place the contract relative
// to the SGroup Atoms
labelLocation = new Vector2();
var sgrpCenter = GeometryUtil.Get2DCenter(sgroupAtoms);
var molCenter = GeometryUtil.Get2DCenter(mol);
var minMax = GeometryUtil.GetMinMax(sgroupAtoms);
var xDiff = sgrpCenter.X - molCenter.X;
var yDiff = sgrpCenter.Y - molCenter.Y;
if (xDiff > 0.1)
{
labelLocation.X = minMax[0]; // min x
label = INTERPUNCT + label;
}
else if (xDiff < -0.1)
{
labelLocation.X = minMax[2]; // max x
label = label + INTERPUNCT;
}
else
{
labelLocation.X = sgrpCenter.X;
label = INTERPUNCT + label;
}
if (yDiff > 0.1)
{
labelLocation.Y = minMax[1]; // min y
}
else if (yDiff < -0.1)
{
labelLocation.Y = minMax[3]; // max y
}
else
{
labelLocation.Y = sgrpCenter.Y;
}
}
var labelgroup = new ElementGroup();
foreach (var outline in atomGenerator.GenerateAbbreviatedSymbol(label, HydrogenPosition.Right)
.Center(labelLocation.X, labelLocation.Y)
.Resize(1 / scale, 1 / -scale)
.GetOutlines())
{
if (highlight != null && style == HighlightStyle.Colored)
{
labelgroup.Add(GeneralPath.ShapeOf(outline, highlight));
}
else
{
labelgroup.Add(GeneralPath.ShapeOf(outline, foreground));
}
}
if (highlight != null && style == HighlightStyle.OuterGlow)
{
var group = new ElementGroup
{
// outer glow needs to be being the label
StandardGenerator.OuterGlow(labelgroup, highlight, glowWidth, stroke),
labelgroup
};
return(group);
}
else
{
return(MarkedElement.MarkupAtom(labelgroup, null));
}
}
/// <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));
}
