public static void IdentifyPlacements(Atom hitAtom, double xamlBondSize, out List <Point> preferredPlacements, int ringSize)
{
Molecule parentMolecule;
parentMolecule = hitAtom.Parent;
Vector direction;
if (hitAtom.Degree != 0)
{
direction = hitAtom.BalancingVector();
}
else
{
direction = BasicGeometry.ScreenNorth;
}
//try to work out exactly where best to place the ring
preferredPlacements = MarkOutAtoms(hitAtom, direction, xamlBondSize, ringSize);
if (parentMolecule.Overlaps(preferredPlacements, new List <Atom> {
hitAtom
}))
{
preferredPlacements = null;
}
}
/// <summary>
/// Draws any implicit hydrogens in the right place
/// </summary>
/// <param name="parentAtom">Owner of the hydrogens</param>
/// <param name="nextPos">Where the insertion point ends up</param>
/// <param name="symbolGeometry">Pre-drawn geometry of the atomic symbol text</param>
/// <param name="nextSymbolPadding">How much space to insert between symbols</param>
/// <returns>geometry of the symbol text plus hydrogens and any subscripts</returns>
private System.Windows.Media.Geometry DrawHydrogens(Atom parentAtom, Point nextPos, System.Windows.Media.Geometry symbolGeometry, double nextSymbolPadding)
{
if (parentAtom.ImplicitHydrogenCount >= 1)
{
System.Windows.Media.Geometry hGeometry;
if (parentAtom.Bonds.Count == 0)
{
hGeometry = DrawHEast(parentAtom, nextPos);
DefaultHOrientation = CompassPoints.East;
}
else if (parentAtom.Bonds.Count == 1)
{
if (Vector.AngleBetween(BasicGeometry.ScreenNorth(),
parentAtom.Bonds[0].OtherAtom(parentAtom).Position - parentAtom.Position) > 0)
//the bond is on the right
{
hGeometry = DrawHWest(parentAtom, nextPos, symbolGeometry, nextSymbolPadding);
DefaultHOrientation = CompassPoints.West;
}
else
{
//default to any old rubbish for now
DefaultHOrientation = CompassPoints.East;
hGeometry = DrawHEast(parentAtom, nextPos);
}
}
else
{
double baFromNorth = Vector.AngleBetween(BasicGeometry.ScreenNorth(),
parentAtom.BalancingVector());
switch (BasicGeometry.SnapTo4NESW(baFromNorth))
{
case CompassPoints.East:
hGeometry = DrawHEast(parentAtom, nextPos);
DefaultHOrientation = CompassPoints.East;
break;
case CompassPoints.North:
hGeometry = DrawHNorth(parentAtom, nextPos, symbolGeometry, nextSymbolPadding);
DefaultHOrientation = CompassPoints.North;
break;
case CompassPoints.South:
hGeometry = DrawHSouth(parentAtom, nextPos, symbolGeometry, nextSymbolPadding);
DefaultHOrientation = CompassPoints.South;
break;
case CompassPoints.West:
hGeometry = DrawHWest(parentAtom, nextPos, symbolGeometry, nextSymbolPadding);
DefaultHOrientation = CompassPoints.West;
break;
default:
hGeometry = DrawHEast(parentAtom, nextPos);
DefaultHOrientation = CompassPoints.East;
break;
}
}
symbolGeometry = new CombinedGeometry(symbolGeometry, hGeometry);
}
return(symbolGeometry);
}
public void CreateFunctionalGroupCharacters(Atom atom, Options options)
{
FunctionalGroup fg = atom.Element as FunctionalGroup;
double baFromNorth = Vector.AngleBetween(BasicGeometry.ScreenNorth, atom.BalancingVector(true));
CompassPoints nesw = BasicGeometry.SnapTo2EW(baFromNorth);
bool reverse = nesw == CompassPoints.West;
#region Set Up Atom Colours
string atomColour = "000000";
if (options.ColouredAtoms)
{
if (!string.IsNullOrEmpty(fg.Colour))
{
atomColour = fg.Colour;
// Strip out # as OoXml does not use it
atomColour = atomColour.Replace("#", "");
}
}
#endregion Set Up Atom Colours
List <FunctionalGroupTerm> terms = fg.ExpandIntoTerms(reverse);
#region Step 1 - Generate the characters and measure Bounding Boxes
var cursorPosition = atom.Position;
List <AtomLabelCharacter> fgCharacters = new List <AtomLabelCharacter>();
TtfCharacter hydrogenCharacter = _TtfCharacterSet['H'];
Rect fgBoundingBox = Rect.Empty;
Rect anchorBoundingBox = Rect.Empty;
foreach (var term in terms)
{
foreach (var part in term.Parts)
{
foreach (char c in part.Text)
{
Rect bb = AddCharacter(c, part.Type);
fgBoundingBox.Union(bb);
if (term.IsAnchor)
{
anchorBoundingBox.Union(bb);
}
}
}
}
#endregion Step 1 - Generate the characters and measure Bounding Boxes
#region Step 2 - Move all characters such that the anchor term is centered on the atom position
double offsetX;
double offsetY;
if (reverse)
{
offsetX = fgBoundingBox.Width - anchorBoundingBox.Width / 2;
offsetY = anchorBoundingBox.Height / 2;
}
else
{
offsetX = anchorBoundingBox.Width / 2;
offsetY = anchorBoundingBox.Height / 2;
}
offsetY = offsetY + anchorBoundingBox.Top - atom.Position.Y;
foreach (var alc in fgCharacters)
{
alc.Position = new Point(alc.Position.X - offsetX, alc.Position.Y - offsetY);
}
#endregion Step 2 - Move all characters such that the anchor term is centered on the atom position
#region Step 3 - Transfer characters into main list
foreach (var alc in fgCharacters)
{
_AtomLabelCharacters.Add(alc);
}
#endregion Step 3 - Transfer characters into main list
#region Step 4 - Convex Hull
_convexhHulls.Add(atom.Path, ConvexHull(atom.Path));
#endregion Step 4 - Convex Hull
// Local Function
Rect AddCharacter(char c, FunctionalGroupPartType type)
{
TtfCharacter ttf = _TtfCharacterSet[c];
var thisCharacterPosition = GetCharacterPosition(cursorPosition, ttf);
var alc = new AtomLabelCharacter(thisCharacterPosition, ttf, atomColour, c, atom.Path, atom.Parent.Path);
alc.IsSubScript = type == FunctionalGroupPartType.Subscript;
alc.IsSuperScript = type == FunctionalGroupPartType.Superscript;
alc.IsSmaller = alc.IsSubScript || alc.IsSuperScript;
Rect thisBoundingBox;
if (alc.IsSmaller)
{
// Start by assuming it's SubScript
thisCharacterPosition.Offset(0, OoXmlHelper.ScaleCsTtfToCml(hydrogenCharacter.Height * OoXmlHelper.SUBSCRIPT_DROP_FACTOR, _meanBondLength));
if (alc.IsSuperScript)
{
// Shift up by height of H to make it SuperScript
thisCharacterPosition.Offset(0, -OoXmlHelper.ScaleCsTtfToCml(hydrogenCharacter.Height, _meanBondLength));
}
// Reset the character's position
alc.Position = thisCharacterPosition;
thisBoundingBox = new Rect(alc.Position,
new Size(OoXmlHelper.ScaleCsTtfToCml(alc.Character.Width, _meanBondLength) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR,
OoXmlHelper.ScaleCsTtfToCml(alc.Character.Height, _meanBondLength) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR));
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(alc.Character.IncrementX, _meanBondLength) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR, 0);
}
else
{
thisBoundingBox = new Rect(alc.Position,
new Size(OoXmlHelper.ScaleCsTtfToCml(alc.Character.Width, _meanBondLength),
OoXmlHelper.ScaleCsTtfToCml(alc.Character.Height, _meanBondLength)));
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(alc.Character.IncrementX, _meanBondLength), 0);
}
fgCharacters.Add(alc);
return(thisBoundingBox);
}
}
public void CreateElementCharacters(Atom atom, Options options)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
//Point atomCentre = new Point((double)atom.X2, (double)atom.Y2);
string atomLabel = atom.Element.Symbol;
Rect labelBounds;
// Get Charge and Isotope values for use later on
int iCharge = atom.FormalCharge ?? 0;
int iAbsCharge = Math.Abs(iCharge);
int isoValue = atom.IsotopeNumber ?? 0;
// Get Implicit Hydrogen Count for use later on
int implicitHCount = atom.ImplicitHydrogenCount;
Point cursorPosition = atom.Position;
Point chargeCursorPosition = atom.Position;
Point isotopeCursorPosition = atom.Position;
double lastOffset = 0;
int bondCount = atom.Bonds.ToList().Count;
#region Decide if atom label is to be displayed
bool showLabel = true;
if (atomLabel == "C")
{
if (atom.ShowSymbol.HasValue)
{
showLabel = atom.ShowSymbol.Value;
}
else
{
if (atom.IsInRing || bondCount > 1)
{
showLabel = false;
}
if (bondCount == 2)
{
Point p1 = atom.Bonds.ToList()[0].OtherAtom(atom).Position;
Point p2 = atom.Bonds.ToList()[1].OtherAtom(atom).Position;
double angle1 = Vector.AngleBetween(-(atom.Position - p1), atom.Position - p2);
if (Math.Abs(angle1) < 8)
{
showLabel = true;
}
}
}
// Force on if atom has charge
if (iAbsCharge > 0)
{
showLabel = true;
}
// Force on if atom has isotope value
if (isoValue > 0)
{
showLabel = true;
}
}
#endregion Decide if atom label is to be displayed
if (showLabel)
{
#region Set Up Atom Colours
string atomColour = "000000";
if (options.ColouredAtoms)
{
if (atom.Element.Colour != null)
{
atomColour = atom.Element.Colour;
// Strip out # as OoXml does not use it
atomColour = atomColour.Replace("#", "");
}
}
#endregion Set Up Atom Colours
#region Step 1 - Measure Bounding Box for all Characters of label
double xMin = double.MaxValue;
double yMin = double.MaxValue;
double xMax = double.MinValue;
double yMax = double.MinValue;
Point thisCharacterPosition;
for (int idx = 0; idx < atomLabel.Length; idx++)
{
char chr = atomLabel[idx];
TtfCharacter c = _TtfCharacterSet[chr];
if (c != null)
{
thisCharacterPosition = GetCharacterPosition(cursorPosition, c);
xMin = Math.Min(xMin, thisCharacterPosition.X);
yMin = Math.Min(yMin, thisCharacterPosition.Y);
xMax = Math.Max(xMax, thisCharacterPosition.X + OoXmlHelper.ScaleCsTtfToCml(c.Width, _meanBondLength));
yMax = Math.Max(yMax, thisCharacterPosition.Y + OoXmlHelper.ScaleCsTtfToCml(c.Height, _meanBondLength));
if (idx < atomLabel.Length - 1)
{
// Move to next Character position
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(c.IncrementX, _meanBondLength), 0);
}
}
}
#endregion Step 1 - Measure Bounding Box for all Characters of label
#region Step 2 - Reset Cursor such that the text is centered about the atom's co-ordinates
double width = xMax - xMin;
double height = yMax - yMin;
cursorPosition = new Point(atom.Position.X - width / 2, atom.Position.Y + height / 2);
chargeCursorPosition = new Point(cursorPosition.X, cursorPosition.Y);
isotopeCursorPosition = new Point(cursorPosition.X, cursorPosition.Y);
labelBounds = new Rect(cursorPosition, new Size(width, height));
#endregion Step 2 - Reset Cursor such that the text is centered about the atom's co-ordinates
#region Step 3 - Place the characters
foreach (char chr in atomLabel)
{
TtfCharacter c = _TtfCharacterSet[chr];
if (c != null)
{
thisCharacterPosition = GetCharacterPosition(cursorPosition, c);
AtomLabelCharacter alc = new AtomLabelCharacter(thisCharacterPosition, c, atomColour, chr, atom.Path, atom.Parent.Path);
_AtomLabelCharacters.Add(alc);
// Move to next Character position
lastOffset = OoXmlHelper.ScaleCsTtfToCml(c.IncrementX, _meanBondLength);
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(c.IncrementX, _meanBondLength), 0);
chargeCursorPosition = new Point(cursorPosition.X, cursorPosition.Y);
}
}
#endregion Step 3 - Place the characters
#region Determine NESW
double baFromNorth = Vector.AngleBetween(BasicGeometry.ScreenNorth, atom.BalancingVector(true));
CompassPoints nesw = CompassPoints.East;
if (bondCount == 1)
{
nesw = BasicGeometry.SnapTo2EW(baFromNorth);
}
else
{
nesw = BasicGeometry.SnapTo4NESW(baFromNorth);
}
#endregion Determine NESW
#region Step 4 - Add Charge if required
if (iCharge != 0)
{
TtfCharacter hydrogenCharacter = _TtfCharacterSet['H'];
char sign = '.';
TtfCharacter chargeSignCharacter = null;
if (iCharge >= 1)
{
sign = '+';
chargeSignCharacter = _TtfCharacterSet['+'];
}
else if (iCharge <= 1)
{
sign = '-';
chargeSignCharacter = _TtfCharacterSet['-'];
}
if (iAbsCharge > 1)
{
string digits = iAbsCharge.ToString();
// Insert digits
foreach (char chr in digits)
{
TtfCharacter chargeValueCharacter = _TtfCharacterSet[chr];
thisCharacterPosition = GetCharacterPosition(chargeCursorPosition, chargeValueCharacter);
// Raise the superscript Character
thisCharacterPosition.Offset(0, -OoXmlHelper.ScaleCsTtfToCml(chargeValueCharacter.Height * OoXmlHelper.CS_SUPERSCRIPT_RAISE_FACTOR, _meanBondLength));
AtomLabelCharacter alcc = new AtomLabelCharacter(thisCharacterPosition, chargeValueCharacter, atomColour, chr, atom.Path, atom.Parent.Path);
alcc.IsSmaller = true;
alcc.IsSubScript = true;
_AtomLabelCharacters.Add(alcc);
// Move to next Character position
chargeCursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(chargeValueCharacter.IncrementX, _meanBondLength) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR, 0);
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(chargeValueCharacter.IncrementX, _meanBondLength) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR, 0);
}
}
// Insert sign at raised position
thisCharacterPosition = GetCharacterPosition(chargeCursorPosition, chargeSignCharacter);
thisCharacterPosition.Offset(0, -OoXmlHelper.ScaleCsTtfToCml(hydrogenCharacter.Height * OoXmlHelper.CS_SUPERSCRIPT_RAISE_FACTOR, _meanBondLength));
thisCharacterPosition.Offset(0, -OoXmlHelper.ScaleCsTtfToCml(chargeSignCharacter.Height / 2 * OoXmlHelper.CS_SUPERSCRIPT_RAISE_FACTOR, _meanBondLength));
AtomLabelCharacter alcs = new AtomLabelCharacter(thisCharacterPosition, chargeSignCharacter, atomColour, sign, atom.Path, atom.Parent.Path);
alcs.IsSmaller = true;
alcs.IsSubScript = true;
_AtomLabelCharacters.Add(alcs);
if (iAbsCharge != 0)
{
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(chargeSignCharacter.IncrementX, _meanBondLength) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR, 0);
}
}
#endregion Step 4 - Add Charge if required
#region Step 5 - Add Implicit H if required
if (options.ShowHydrogens && implicitHCount > 0)
{
TtfCharacter hydrogenCharacter = _TtfCharacterSet['H'];
string numbers = "012345";
TtfCharacter implicitValueCharacter = _TtfCharacterSet[numbers[implicitHCount]];
#region Add H
if (hydrogenCharacter != null)
{
switch (nesw)
{
case CompassPoints.North:
if (atom.Bonds.ToList().Count > 1)
{
cursorPosition.X = labelBounds.X
+ (labelBounds.Width / 2)
- (OoXmlHelper.ScaleCsTtfToCml(hydrogenCharacter.Width, _meanBondLength) / 2);
cursorPosition.Y = cursorPosition.Y
+ OoXmlHelper.ScaleCsTtfToCml(-hydrogenCharacter.Height, _meanBondLength)
- OoXmlHelper.CHARACTER_VERTICAL_SPACING;
if (iCharge > 0)
{
if (implicitHCount > 1)
{
cursorPosition.Offset(0,
OoXmlHelper.ScaleCsTtfToCml(
-implicitValueCharacter.Height *
OoXmlHelper.SUBSCRIPT_SCALE_FACTOR / 2, _meanBondLength)
- OoXmlHelper.CHARACTER_VERTICAL_SPACING);
}
}
}
break;
case CompassPoints.East:
// Leave as is
break;
case CompassPoints.South:
if (atom.Bonds.ToList().Count > 1)
{
cursorPosition.X = labelBounds.X + (labelBounds.Width / 2)
- (OoXmlHelper.ScaleCsTtfToCml(hydrogenCharacter.Width, _meanBondLength) / 2);
cursorPosition.Y = cursorPosition.Y
+ OoXmlHelper.ScaleCsTtfToCml(hydrogenCharacter.Height, _meanBondLength)
+ OoXmlHelper.CHARACTER_VERTICAL_SPACING;
}
break;
case CompassPoints.West:
if (implicitHCount == 1)
{
if (iAbsCharge == 0)
{
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(-(hydrogenCharacter.IncrementX * 2), _meanBondLength), 0);
}
else
{
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(-((hydrogenCharacter.IncrementX * 2 + implicitValueCharacter.IncrementX * 1.25)), _meanBondLength), 0);
}
}
else
{
if (iAbsCharge == 0)
{
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(-(hydrogenCharacter.IncrementX * 2.5), _meanBondLength), 0);
}
else
{
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(-((hydrogenCharacter.IncrementX * 2 + implicitValueCharacter.IncrementX * 1.25)), _meanBondLength), 0);
}
}
break;
}
thisCharacterPosition = GetCharacterPosition(cursorPosition, hydrogenCharacter);
AtomLabelCharacter alc = new AtomLabelCharacter(thisCharacterPosition, hydrogenCharacter, atomColour, 'H', atom.Path, atom.Parent.Path);
_AtomLabelCharacters.Add(alc);
// Move to next Character position
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(hydrogenCharacter.IncrementX, _meanBondLength), 0);
if (nesw == CompassPoints.East)
{
chargeCursorPosition = new Point(cursorPosition.X, cursorPosition.Y);
}
if (nesw == CompassPoints.West)
{
isotopeCursorPosition = new Point(thisCharacterPosition.X, isotopeCursorPosition.Y);
}
}
#endregion Add H
#region Add number
if (implicitHCount > 1)
{
if (implicitValueCharacter != null)
{
thisCharacterPosition = GetCharacterPosition(cursorPosition, implicitValueCharacter);
// Drop the subscript Character
thisCharacterPosition.Offset(0, OoXmlHelper.ScaleCsTtfToCml(hydrogenCharacter.Width * OoXmlHelper.SUBSCRIPT_DROP_FACTOR, _meanBondLength));
AtomLabelCharacter alc = new AtomLabelCharacter(thisCharacterPosition, implicitValueCharacter, atomColour, numbers[implicitHCount], atom.Path, atom.Parent.Path);
alc.IsSmaller = true;
alc.IsSubScript = true;
_AtomLabelCharacters.Add(alc);
// Move to next Character position
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(implicitValueCharacter.IncrementX, _meanBondLength) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR, 0);
}
}
#endregion Add number
}
#endregion Step 5 - Add Implicit H if required
#region Step 6 - Add IsoTope Number if required
if (isoValue > 0)
{
string digits = isoValue.ToString();
xMin = double.MaxValue;
yMin = double.MaxValue;
xMax = double.MinValue;
yMax = double.MinValue;
Point isoOrigin = isotopeCursorPosition;
// Calculate width of digits
foreach (char chr in digits)
{
TtfCharacter c = _TtfCharacterSet[chr];
thisCharacterPosition = GetCharacterPosition(isotopeCursorPosition, c);
// Raise the superscript Character
thisCharacterPosition.Offset(0, -OoXmlHelper.ScaleCsTtfToCml(c.Height * OoXmlHelper.CS_SUPERSCRIPT_RAISE_FACTOR, _meanBondLength));
xMin = Math.Min(xMin, thisCharacterPosition.X);
yMin = Math.Min(yMin, thisCharacterPosition.Y);
xMax = Math.Max(xMax, thisCharacterPosition.X + OoXmlHelper.ScaleCsTtfToCml(c.Width, _meanBondLength));
yMax = Math.Max(yMax, thisCharacterPosition.Y + OoXmlHelper.ScaleCsTtfToCml(c.Height, _meanBondLength));
// Move to next Character position
isotopeCursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(c.IncrementX, _meanBondLength) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR, 0);
}
// Re-position Isotope Cursor
width = xMax - xMin;
isotopeCursorPosition = new Point(isoOrigin.X - width, isoOrigin.Y);
// Insert digits
foreach (char chr in digits)
{
TtfCharacter c = _TtfCharacterSet[chr];
thisCharacterPosition = GetCharacterPosition(isotopeCursorPosition, c);
// Raise the superscript Character
thisCharacterPosition.Offset(0, -OoXmlHelper.ScaleCsTtfToCml(c.Height * OoXmlHelper.CS_SUPERSCRIPT_RAISE_FACTOR, _meanBondLength));
AtomLabelCharacter alcc = new AtomLabelCharacter(thisCharacterPosition, c, atomColour, chr, atom.Path, atom.Parent.Path);
alcc.IsSmaller = true;
alcc.IsSubScript = true;
_AtomLabelCharacters.Add(alcc);
// Move to next Character position
isotopeCursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(c.IncrementX, _meanBondLength) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR, 0);
}
}
#endregion Step 6 - Add IsoTope Number if required
#region Step 7 - Create Convex Hull
_convexhHulls.Add(atom.Path, ConvexHull(atom.Path));
#endregion Step 7 - Create Convex Hull
}
}
public void CreateCharacters(Atom atom, Options options)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
//Debug.WriteLine("Atom: " + atom.Id + " is " + atom.ElementType);
string atomLabel = atom.Element.Symbol;
Rect labelBounds;
// Get Charge and Isotope valuesfor use later on
int iCharge = atom.FormalCharge ?? 0;
int iAbsCharge = Math.Abs(iCharge);
int isoValue = atom.IsotopeNumber ?? 0;
// Get Implicit Hydrogen Count for use later on
int implicitHCount = atom.ImplicitHydrogenCount;
Point cursorPosition = atom.Position;
Point chargeCursorPosition = atom.Position;
Point isotopeCursorPosition = atom.Position;
double lastOffset = 0;
//Debug.WriteLine(" X: " + atom.X2 + " Y: " + atom.Y2 + " Implicit H Count: " + implicitHCount);
int ringCount = atom.Rings.Count();
int bondCount = atom.Bonds.Count;
//var bv = atom.BalancingVector();
//_telemetry.Write(module, "Debugging", $"Atom {atomLabel} [{atom.Id}] at {atom.Position} BalancingVector {bv} [{CoordinateTool.BearingOfVector(bv)}°]");
#region Decide if atom label is to be displayed
bool showLabel = true;
if (atomLabel == "C")
{
if (!options.ShowCarbons)
{
if (ringCount > 0 || bondCount > 1)
{
showLabel = false;
}
if (bondCount == 2)
{
Point p1 = atom.Bonds[0].OtherAtom(atom).Position;
Point p2 = atom.Bonds[1].OtherAtom(atom).Position;
double angle1 = Vector.AngleBetween(-(atom.Position - p1), atom.Position - p2);
if (Math.Abs(angle1) < 8)
{
showLabel = true;
}
}
// Force on if atom has charge
if (iAbsCharge > 0)
{
showLabel = true;
}
// Force on if atom has isotope value
if (isoValue > 0)
{
showLabel = true;
}
}
}
#endregion Decide if atom label is to be displayed
if (showLabel)
{
#region Set Up Atom Colours
string atomColour = "000000";
if (options.ColouredAtoms)
{
if ((atom.Element as Element).Colour != null)
{
atomColour = ((Element)atom.Element).Colour;
// Strip out # as OoXml does not use it
atomColour = atomColour.Replace("#", "");
}
}
#endregion Set Up Atom Colours
#region Step 1 - Measure Bounding Box for all Characters of label
double xMin = double.MaxValue;
double yMin = double.MaxValue;
double xMax = double.MinValue;
double yMax = double.MinValue;
Point thisCharacterPosition;
for (int idx = 0; idx < atomLabel.Length; idx++)
{
char chr = atomLabel[idx];
TtfCharacter c = _TtfCharacterSet[chr];
if (c != null)
{
thisCharacterPosition = GetCharacterPosition(cursorPosition, c);
xMin = Math.Min(xMin, thisCharacterPosition.X);
yMin = Math.Min(yMin, thisCharacterPosition.Y);
xMax = Math.Max(xMax, thisCharacterPosition.X + OoXmlHelper.ScaleCsTtfToCml(c.Width));
yMax = Math.Max(yMax, thisCharacterPosition.Y + OoXmlHelper.ScaleCsTtfToCml(c.Height));
// Uncomment the following to disable offsetting for terminal atoms
//if (bonds.Count == 1)
//{
// break;
//}
if (idx < atomLabel.Length - 1)
{
// Move to next Character position
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(c.IncrementX), 0);
}
}
}
#endregion Step 1 - Measure Bounding Box for all Characters of label
#region Step 2 - Reset Cursor such that the text is centered about the atom's co-ordinates
double width = xMax - xMin;
double height = yMax - yMin;
cursorPosition = new Point(atom.Position.X - width / 2, atom.Position.Y + height / 2);
chargeCursorPosition = new Point(cursorPosition.X, cursorPosition.Y);
isotopeCursorPosition = new Point(cursorPosition.X, cursorPosition.Y);
labelBounds = new Rect(cursorPosition, new Size(width, height));
//_telemetry.Write(module, "Debugging", $"Atom {atomLabel} [{atom.Id}] Label Bounds {labelBounds}");
#endregion Step 2 - Reset Cursor such that the text is centered about the atom's co-ordinates
#region Step 3 - Place the characters
foreach (char chr in atomLabel)
{
TtfCharacter c = _TtfCharacterSet[chr];
if (c != null)
{
thisCharacterPosition = GetCharacterPosition(cursorPosition, c);
AtomLabelCharacter alc = new AtomLabelCharacter(thisCharacterPosition, c, atomColour, chr, atom.Id, atom.Parent.Id);
_AtomLabelCharacters.Add(alc);
// Move to next Character position
lastOffset = OoXmlHelper.ScaleCsTtfToCml(c.IncrementX);
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(c.IncrementX), 0);
chargeCursorPosition = new Point(cursorPosition.X, cursorPosition.Y);
}
}
#endregion Step 3 - Place the characters
#region Determine NESW
double baFromNorth = Vector.AngleBetween(BasicGeometry.ScreenNorth(), atom.BalancingVector(true));
CompassPoints nesw = CompassPoints.East;
if (bondCount == 1)
{
nesw = BasicGeometry.SnapTo2EW(baFromNorth);
}
else
{
nesw = BasicGeometry.SnapTo4NESW(baFromNorth);
}
#endregion Determine NESW
#region Step 4 - Add Charge if required
if (iCharge != 0)
{
TtfCharacter hydrogenCharacter = _TtfCharacterSet['H'];
char sign = '.';
TtfCharacter chargeSignCharacter = null;
if (iCharge >= 1)
{
sign = '+';
chargeSignCharacter = _TtfCharacterSet['+'];
}
else if (iCharge <= 1)
{
sign = '-';
chargeSignCharacter = _TtfCharacterSet['-'];
}
if (iAbsCharge > 1)
{
string digits = iAbsCharge.ToString();
// Insert digits
foreach (char chr in digits)
{
TtfCharacter chargeValueCharacter = _TtfCharacterSet[chr];
thisCharacterPosition = GetCharacterPosition(chargeCursorPosition, chargeValueCharacter);
// Raise the superscript Character
thisCharacterPosition.Offset(0, -OoXmlHelper.ScaleCsTtfToCml(chargeValueCharacter.Height * OoXmlHelper.CS_SUPERSCRIPT_RAISE_FACTOR));
AtomLabelCharacter alcc = new AtomLabelCharacter(thisCharacterPosition, chargeValueCharacter, atomColour, chr, atom.Id, atom.Parent.Id);
alcc.IsSubScript = true;
_AtomLabelCharacters.Add(alcc);
// Move to next Character position
chargeCursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(chargeValueCharacter.IncrementX) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR, 0);
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(chargeValueCharacter.IncrementX) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR, 0);
}
}
// Insert sign at raised position
thisCharacterPosition = GetCharacterPosition(chargeCursorPosition, chargeSignCharacter);
thisCharacterPosition.Offset(0, -OoXmlHelper.ScaleCsTtfToCml(hydrogenCharacter.Height * OoXmlHelper.CS_SUPERSCRIPT_RAISE_FACTOR));
thisCharacterPosition.Offset(0, -OoXmlHelper.ScaleCsTtfToCml(chargeSignCharacter.Height / 2 * OoXmlHelper.CS_SUPERSCRIPT_RAISE_FACTOR));
AtomLabelCharacter alcs = new AtomLabelCharacter(thisCharacterPosition, chargeSignCharacter, atomColour, sign, atom.Id, atom.Parent.Id);
alcs.IsSubScript = true;
_AtomLabelCharacters.Add(alcs);
if (iAbsCharge != 0)
{
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(chargeSignCharacter.IncrementX) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR, 0);
}
}
#endregion Step 4 - Add Charge if required
#region Step 5 - Add Implicit H if required
if (options.ShowHydrogens && implicitHCount > 0)
{
TtfCharacter hydrogenCharacter = _TtfCharacterSet['H'];
string numbers = "012345";
TtfCharacter implicitValueCharacter = _TtfCharacterSet[numbers[implicitHCount]];
#region Add H
if (hydrogenCharacter != null)
{
switch (nesw)
{
case CompassPoints.North:
if (atom.Bonds.Count > 1)
{
cursorPosition.X = labelBounds.X + (labelBounds.Width / 2) - (OoXmlHelper.ScaleCsTtfToCml(hydrogenCharacter.Width) / 2);
cursorPosition.Y = cursorPosition.Y +
OoXmlHelper.ScaleCsTtfToCml(-hydrogenCharacter.Height) -
OoXmlHelper.CHARACTER_CLIPPING_MARGIN;
if (iCharge > 0)
{
if (implicitHCount > 1)
{
cursorPosition.Offset(0, OoXmlHelper.ScaleCsTtfToCml(-implicitValueCharacter.Height * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR / 2) - OoXmlHelper.CHARACTER_CLIPPING_MARGIN);
}
}
}
break;
case CompassPoints.East:
// Leave as is
break;
case CompassPoints.South:
if (atom.Bonds.Count > 1)
{
cursorPosition.X = labelBounds.X + (labelBounds.Width / 2) - (OoXmlHelper.ScaleCsTtfToCml(hydrogenCharacter.Width) / 2);
cursorPosition.Y = cursorPosition.Y +
OoXmlHelper.ScaleCsTtfToCml(hydrogenCharacter.Height) +
OoXmlHelper.CHARACTER_CLIPPING_MARGIN;
}
break;
case CompassPoints.West:
if (implicitHCount == 1)
{
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(-(hydrogenCharacter.IncrementX * 2)), 0);
}
else
{
if (iAbsCharge == 0)
{
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(-(hydrogenCharacter.IncrementX * 2.5)), 0);
}
else
{
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(-((hydrogenCharacter.IncrementX * 2 + implicitValueCharacter.IncrementX * 1.5))), 0);
}
}
break;
}
//_telemetry.Write(module, "Debugging", $"Adding H at {cursorPosition}");
thisCharacterPosition = GetCharacterPosition(cursorPosition, hydrogenCharacter);
AtomLabelCharacter alc = new AtomLabelCharacter(thisCharacterPosition, hydrogenCharacter, atomColour, 'H', atom.Id, atom.Parent.Id);
_AtomLabelCharacters.Add(alc);
// Move to next Character position
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(hydrogenCharacter.IncrementX), 0);
if (nesw == CompassPoints.East)
{
chargeCursorPosition = new Point(cursorPosition.X, cursorPosition.Y);
}
if (nesw == CompassPoints.West)
{
isotopeCursorPosition = new Point(thisCharacterPosition.X, isotopeCursorPosition.Y);
}
}
#endregion Add H
#region Add number
if (implicitHCount > 1)
{
if (implicitValueCharacter != null)
{
thisCharacterPosition = GetCharacterPosition(cursorPosition, implicitValueCharacter);
// Drop the subscript Character
thisCharacterPosition.Offset(0, OoXmlHelper.ScaleCsTtfToCml(hydrogenCharacter.Width * OoXmlHelper.SUBSCRIPT_DROP_FACTOR));
AtomLabelCharacter alc = new AtomLabelCharacter(thisCharacterPosition, implicitValueCharacter, atomColour, numbers[implicitHCount], atom.Id, atom.Parent.Id);
alc.IsSubScript = true;
_AtomLabelCharacters.Add(alc);
// Move to next Character position
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(implicitValueCharacter.IncrementX) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR, 0);
}
}
#endregion Add number
}
#endregion Step 5 - Add Implicit H if required
#region Step 6 - Add IsoTope Number if required
if (isoValue > 0)
{
string digits = isoValue.ToString();
xMin = double.MaxValue;
yMin = double.MaxValue;
xMax = double.MinValue;
yMax = double.MinValue;
Point isoOrigin = isotopeCursorPosition;
// Calculate width of digits
foreach (char chr in digits)
{
TtfCharacter c = _TtfCharacterSet[chr];
thisCharacterPosition = GetCharacterPosition(isotopeCursorPosition, c);
// Raise the superscript Character
thisCharacterPosition.Offset(0, -OoXmlHelper.ScaleCsTtfToCml(c.Height * OoXmlHelper.CS_SUPERSCRIPT_RAISE_FACTOR));
xMin = Math.Min(xMin, thisCharacterPosition.X);
yMin = Math.Min(yMin, thisCharacterPosition.Y);
xMax = Math.Max(xMax, thisCharacterPosition.X + OoXmlHelper.ScaleCsTtfToCml(c.Width));
yMax = Math.Max(yMax, thisCharacterPosition.Y + OoXmlHelper.ScaleCsTtfToCml(c.Height));
// Move to next Character position
isotopeCursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(c.IncrementX) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR, 0);
}
// Re-position Isotope Cursor
width = xMax - xMin;
isotopeCursorPosition = new Point(isoOrigin.X - width, isoOrigin.Y);
// Insert digits
foreach (char chr in digits)
{
TtfCharacter c = _TtfCharacterSet[chr];
thisCharacterPosition = GetCharacterPosition(isotopeCursorPosition, c);
// Raise the superscript Character
thisCharacterPosition.Offset(0, -OoXmlHelper.ScaleCsTtfToCml(c.Height * OoXmlHelper.CS_SUPERSCRIPT_RAISE_FACTOR));
AtomLabelCharacter alcc = new AtomLabelCharacter(thisCharacterPosition, c, atomColour, chr, atom.Id, atom.Parent.Id);
alcc.IsSubScript = true;
_AtomLabelCharacters.Add(alcc);
// Move to next Character position
isotopeCursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(c.IncrementX) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR, 0);
}
}
#endregion Step 6 - Add IsoTope Number if required
#region Step 7 - Create Convex Hull
List <Point> points = new List <Point>();
var chars = _AtomLabelCharacters.Where(m => m.ParentAtom == atom.Id);
double margin = OoXmlHelper.CHARACTER_CLIPPING_MARGIN;
foreach (var c in chars)
{
// Top Left --
points.Add(new Point(c.Position.X - margin, c.Position.Y - margin));
if (c.IsSubScript)
{
// Top Right +-
points.Add(new Point(c.Position.X + OoXmlHelper.ScaleCsTtfToCml(c.Character.Width) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR + margin,
c.Position.Y - margin));
// Bottom Right ++
points.Add(new Point(c.Position.X + OoXmlHelper.ScaleCsTtfToCml(c.Character.Width) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR + margin,
c.Position.Y + OoXmlHelper.ScaleCsTtfToCml(c.Character.Height) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR + margin));
// Bottom Left -+
points.Add(new Point(c.Position.X - margin,
c.Position.Y + OoXmlHelper.ScaleCsTtfToCml(c.Character.Height) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR + margin));
}
else
{
// Top Right +-
points.Add(new Point(c.Position.X + OoXmlHelper.ScaleCsTtfToCml(c.Character.Width) + margin,
c.Position.Y - margin));
// Bottom Right ++
points.Add(new Point(c.Position.X + OoXmlHelper.ScaleCsTtfToCml(c.Character.Width) + margin,
c.Position.Y + OoXmlHelper.ScaleCsTtfToCml(c.Character.Height) + margin));
// Bottom Left -+
points.Add(new Point(c.Position.X - margin,
c.Position.Y + OoXmlHelper.ScaleCsTtfToCml(c.Character.Height) + margin));
}
}
_convexhHulls.Add(atom.Id, GeometryTool.MakeConvexHull(points));
#endregion Step 7 - Create Convex Hull
}
}