public void AdenineRingPreference()
{
var adenine = TestMoleculeFactory.MakeAdenine();
var ringMap = StandardBondGenerator.RingPreferenceMap(adenine);
int nSize5 = 0, nSize6 = 0;
foreach (var bond in adenine.Bonds)
{
if (!ringMap.TryGetValue(bond, out IAtomContainer ring))
{
continue;// exocyclic bond
}
switch (ring.Atoms.Count)
{
case 5:
nSize5++;
break;
case 6:
nSize6++;
break;
}
}
// 6 bonds should point to the six member ring
// 4 bonds should point to the five member ring
Assert.AreEqual(4, nSize5);
Assert.AreEqual(6, nSize6);
}
public void MetalRingPreference()
{
var smipar = CDK.SmilesParser;
var mol = smipar.ParseSmiles("C1[Fe]C=CC2=C1C=CN2");
foreach (var atom in mol.Atoms)
{
atom.Point2D = new Vector2(0, 0);
}
var ringMap = StandardBondGenerator.RingPreferenceMap(mol);
int nSize5 = 0, nSize6 = 0;
foreach (var bond in mol.Bonds)
{
var ring = ringMap[bond];
// exocyclic bond
if (ring == null)
{
continue;
}
switch (ring.Atoms.Count)
{
case 5:
nSize5++;
break;
case 6:
nSize6++;
break;
}
}
// 5 bonds should point to the six member ring
// 5 bonds should point to the five member ring
Assert.AreEqual(5, nSize5);
Assert.AreEqual(5, nSize6);
}
/// <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));
}
