public void useDefaultPlacementWithNoBonds()
{
var mock_atom = new Mock <IAtom>(); var atom = mock_atom.Object;
mock_atom.Setup(n => n.AtomicNumber).Returns(8);
Assert.AreEqual(Left, HydrogenPositionTools.Position(atom, Array.Empty <IAtom>()));
}
public void HydrogensAppearBeforeSulfur()
{
var mock_atom = new Mock <IAtom>(); var atom = mock_atom.Object;
mock_atom.Setup(n => n.AtomicNumber).Returns(16);
Assert.AreEqual(Left, HydrogenPositionTools.UsingDefaultPlacement(atom));
}
public void HydrogensAppearAfterCarbon()
{
var mock_atom = new Mock <IAtom>(); var atom = mock_atom.Object;
mock_atom.Setup(n => n.AtomicNumber).Returns(6);
Assert.AreEqual(Right, HydrogenPositionTools.UsingDefaultPlacement(atom));
}
public void HydrogensAppearBeforeWhenBondIsFromRight()
{
var mock_atom1 = new Mock <IAtom>(); var atom1 = mock_atom1.Object;
var mock_atom2 = new Mock <IAtom>(); var atom2 = mock_atom2.Object;
mock_atom1.Setup(n => n.Point2D).Returns(new Vector2(0, 0));
mock_atom2.Setup(n => n.Point2D).Returns(new Vector2(1, 0));
Assert.AreEqual(Left, HydrogenPositionTools.Position(atom1, new[] { atom2 }));
}
public void Symmetric()
{
// all extents are the same so 'Right' is chosen in preference
var vectors = new[]
{
new Vector2(1, 1), new Vector2(1, -1), new Vector2(-1, 1), new Vector2(-1, -1)
};
Assert.AreEqual(Right, HydrogenPositionTools.UsingAngularExtent(vectors));
}
public void UsingCardinalDirection()
{
var mock_atom1 = new Mock <IAtom>(); var atom1 = mock_atom1.Object;
var mock_atom2 = new Mock <IAtom>(); var atom2 = mock_atom2.Object;
var mock_atom3 = new Mock <IAtom>(); var atom3 = mock_atom2.Object;
mock_atom1.Setup(n => n.Point2D).Returns(new Vector2(0, 0));
mock_atom2.Setup(n => n.Point2D).Returns(new Vector2(1, 1));
mock_atom3.Setup(n => n.Point2D).Returns(new Vector2(1, -1));
Assert.AreEqual(Left, HydrogenPositionTools.Position(atom1, new[] { atom2, atom3 }));
}
public void AngularExtentLeft()
{
double theta = Vectors.DegreeToRadian(120);
var vectors = new[]
{
new Vector2(1, 0),
new Vector2(Math.Cos(theta), Math.Sin(theta)),
new Vector2(Math.Cos(-theta), Math.Sin(-theta)),
};
Assert.AreEqual(Left, HydrogenPositionTools.UsingAngularExtent(vectors));
}
public void LargestExtent()
{
// the largest extents here are above and below
var vectors = new[]
{
new Vector2(Math.Cos(Vectors.DegreeToRadian(30)), Math.Sin(Vectors.DegreeToRadian(30))),
new Vector2(Math.Cos(Vectors.DegreeToRadian(-30)), Math.Sin(Vectors.DegreeToRadian(-30))),
new Vector2(Math.Cos(Vectors.DegreeToRadian(150)), Math.Sin(Vectors.DegreeToRadian(150))),
new Vector2(Math.Cos(Vectors.DegreeToRadian(-150)), Math.Sin(Vectors.DegreeToRadian(-150)))
};
Assert.AreEqual(Above, HydrogenPositionTools.UsingAngularExtent(vectors));
}
public void AngularExtentAbove()
{
double theta1 = Vectors.DegreeToRadian(30);
double theta2 = Vectors.DegreeToRadian(150);
var vectors = new[]
{
new Vector2(0, -1),
new Vector2(Math.Cos(theta1), Math.Sin(theta1)),
new Vector2(Math.Cos(theta2), Math.Sin(theta2)),
};
Assert.AreEqual(Above, HydrogenPositionTools.UsingAngularExtent(vectors));
}
public void CardinalDirectionForNorthWestIsRight()
{
Assert.AreEqual(Right, HydrogenPositionTools.UsingCardinalDirection(new Vector2(-1, 0)));
}
public void CardinalDirectionForSouthIsAbove()
{
Assert.AreEqual(Above, HydrogenPositionTools.UsingCardinalDirection(new Vector2(0, -1)));
}
public void CardinalDirectionForSouthEastIsLeft()
{
Assert.AreEqual(Left, HydrogenPositionTools.UsingCardinalDirection(new Vector2(1, -1)));
}
public void CardinalDirectionForNorthIsBelow()
{
Assert.AreEqual(Below, HydrogenPositionTools.UsingCardinalDirection(new Vector2(0, 1)));
}
public void ValueOf()
{
Assert.AreEqual(HydrogenPosition.Above, HydrogenPositionTools.Parse("Above"));
}
/// <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);
}