/** {@inheritDoc} */
@Override
@TestMethod("testEmptyReaction")
public IRenderingElement generate(IReaction reaction, RendererModel model) {
if (!model.getParameter(ShowReactionBoxes.class).getValue()) return null;
double separation =
model.getParameter(BondLength.class).getValue()
/ model.getParameter(Scale.class).getValue();
Rectangle2D totalBounds = BoundsCalculator.calculateBounds(reaction);
if (totalBounds == null) return null;
ElementGroup diagram = new ElementGroup();
Color foregroundColor =
model.getParameter(BasicSceneGenerator.ForegroundColor.class).getValue();
diagram.add(
new RectangleElement(
totalBounds.getMinX() - separation,
totalBounds.getMinY() - separation,
totalBounds.getMaxX() + separation,
totalBounds.getMaxY() + separation,
foregroundColor));
if (reaction.getID() != null) {
diagram.add(
new TextElement(
(totalBounds.getMinX() + totalBounds.getMaxX()) / 2,
totalBounds.getMinY() - separation,
reaction.getID(),
foregroundColor));
}
return diagram;
}
public IRenderingElement generate(IAtomContainer ac, RendererModel model) {
if (generators == null) return EMPTY_ELEMENT;
if (use) {
ElementGroup group = new ElementGroup();
for (IGenerator generator : generators) {
group.add(generator.generate(ac, model));
}
return group;
} else return EMPTY_ELEMENT;
}
private IRenderingElement generate(IAtomContainer molecule, RendererModel model, int atomNum)
throws CDKException {
// tag the atom and bond ids
String molId = molecule.getProperty(MarkedElement.ID_KEY);
if (molId != null) {
int atomId = 0, bondid = 0;
for (IAtom atom : molecule.atoms())
setIfMissing(atom, MarkedElement.ID_KEY, molId + "atm" + ++atomId);
for (IBond bond : molecule.bonds())
setIfMissing(bond, MarkedElement.ID_KEY, molId + "bnd" + ++bondid);
}
if (annotateAtomNum) {
for (IAtom atom : molecule.atoms()) {
if (atom.getProperty(StandardGenerator.ANNOTATION_LABEL) != null)
throw new UnsupportedOperationException("Multiple annotation labels are not supported.");
atom.setProperty(StandardGenerator.ANNOTATION_LABEL, Integer.toString(atomNum++));
}
} else if (annotateAtomVal) {
for (IAtom atom : molecule.atoms()) {
if (atom.getProperty(StandardGenerator.ANNOTATION_LABEL) != null)
throw new UnsupportedOperationException("Multiple annotation labels are not supported.");
atom.setProperty(
StandardGenerator.ANNOTATION_LABEL, atom.getProperty(CDKConstants.COMMENT));
}
} else if (annotateAtomMap) {
for (IAtom atom : molecule.atoms()) {
if (atom.getProperty(StandardGenerator.ANNOTATION_LABEL) != null)
throw new UnsupportedOperationException("Multiple annotation labels are not supported.");
int mapidx = accessAtomMap(atom);
if (mapidx > 0) {
atom.setProperty(StandardGenerator.ANNOTATION_LABEL, Integer.toString(mapidx));
}
}
}
ElementGroup grp = new ElementGroup();
for (IGenerator<IAtomContainer> gen : gens) grp.add(gen.generate(molecule, model));
// cleanup
if (annotateAtomNum || annotateAtomMap) {
for (IAtom atom : molecule.atoms()) {
atom.removeProperty(StandardGenerator.ANNOTATION_LABEL);
}
}
return grp;
}
/* (non-Javadoc)
* @see org.openscience.cdk.renderer.generators.IGenerator#generate(org.openscience.cdk.interfaces.IAtomContainer, org.openscience.cdk.renderer.RendererModel)
*/
public IRenderingElement generate(IAtomContainer ac, RendererModel model) {
double r = model.getHighlightDistance() / model.getScale();
ElementGroup group = new ElementGroup();
for (ISubStructure subStructure : subStructures) {
ElementGroup subGroup = new ElementGroup();
if (subStructure.getAtomContainer() == null) continue;
for (IAtom atom : subStructure.getAtomContainer().atoms()) {
Point2d p = atom.getPoint2d();
Color color = subStructure.getHighlightingColor(atom);
subGroup.add(generateElement(p, r, color != null ? color : DEFAULT_COLOR));
}
group.add(subGroup);
}
return group;
}
private IRenderingElement generateAbbreviationSgroup(Sgroup sgroup) {
String label = sgroup.getSubscript();
// already handled by symbol remapping
if (sgroup.getBonds().size() > 0 || label == null || label.isEmpty()) {
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
final Point2d labelCoords = GeometryUtil.get2DCenter(sgroup.getAtoms());
ElementGroup group = new ElementGroup();
for (Shape outline :
atomGenerator
.generatePseudoSymbol(label, HydrogenPosition.Right)
.resize(1 / scale, 1 / -scale)
.getOutlines()) group.add(GeneralPath.shapeOf(outline, foreground));
return MarkedElement.markupAtom(group, null);
}
/**
* Generate the Sgroup elements for the provided atom contains.
*
* @param container molecule
* @return Sgroup rendering elements
*/
IRenderingElement generateSgroups(IAtomContainer container) {
ElementGroup result = new ElementGroup();
List<Sgroup> sgroups = container.getProperty(CDKConstants.CTAB_SGROUPS);
if (sgroups == null || sgroups.isEmpty()) return result;
for (Sgroup sgroup : sgroups) {
switch (sgroup.getType()) {
case CtabAbbreviation:
result.add(generateAbbreviationSgroup(sgroup));
break;
case CtabMultipleGroup:
result.add(generateMultipleSgroup(sgroup));
break;
case CtabAnyPolymer:
case CtabMonomer:
case CtabCrossLink:
case CtabCopolymer:
case CtabStructureRepeatUnit:
case CtabMer:
case CtabGraft:
case CtabModified:
result.add(generatePolymerSgroup(sgroup));
break;
case CtabComponent:
case CtabMixture:
case CtabFormulation:
result.add(generateMixtureSgroup(sgroup));
break;
case CtabGeneric:
// not strictly a polymer but okay to draw as one
result.add(generatePolymerSgroup(sgroup));
break;
}
}
return result;
}
private IRenderingElement generateSgroupBrackets(
Sgroup sgroup,
List<SgroupBracket> brackets,
String subscriptSuffix,
String superscriptSuffix) {
// brackets are square by default (style:0)
Integer style = sgroup.getValue(SgroupKey.CtabBracketStyle);
boolean round = style != null && style == 1;
ElementGroup result = new ElementGroup();
Set<IAtom> atoms = sgroup.getAtoms();
Set<IBond> crossingBonds = sgroup.getBonds();
// easy to depict in correct orientation, we just
// point each bracket at the atom of a crossing
// bond that is 'in' the group - this scales
// to more than two brackets
// first we need to pair the brackets with the bonds
Map<SgroupBracket, IBond> pairs =
crossingBonds.size() == brackets.size()
? bracketBondPairs(brackets, crossingBonds)
: Collections.<SgroupBracket, IBond>emptyMap();
if (!pairs.isEmpty()) {
SgroupBracket suffixBracket = null;
Vector2d suffixBracketPerp = null;
for (Map.Entry<SgroupBracket, IBond> e : pairs.entrySet()) {
final SgroupBracket bracket = e.getKey();
final IBond bond = e.getValue();
final IAtom inGroupAtom =
atoms.contains(bond.getAtom(0)) ? bond.getAtom(0) : bond.getAtom(1);
final Point2d p1 = bracket.getFirstPoint();
final Point2d p2 = bracket.getSecondPoint();
final Vector2d perp = VecmathUtil.newPerpendicularVector(VecmathUtil.newUnitVector(p1, p2));
// point the vector at the atom group
Point2d midpoint = VecmathUtil.midpoint(p1, p2);
if (perp.dot(VecmathUtil.newUnitVector(midpoint, inGroupAtom.getPoint2d())) < 0) {
perp.negate();
}
perp.scale(bracketDepth);
Path2D path = new Path2D.Double();
if (round) {
// bracket 1 (cp: control point)
path.moveTo(p1.x + perp.x, p1.y + perp.y);
Point2d cpb1 = new Point2d(midpoint);
cpb1.add(VecmathUtil.negate(perp));
path.quadTo(cpb1.x, cpb1.y, p2.x + perp.x, p2.y + p2.y);
} else {
path.moveTo(p1.x + perp.x, p1.y + perp.y);
path.lineTo(p1.x, p1.y);
path.lineTo(p2.x, p2.y);
path.lineTo(p2.x + perp.x, p2.y + perp.y);
}
result.add(GeneralPath.outlineOf(path, stroke, foreground));
if (suffixBracket == null) {
suffixBracket = bracket;
suffixBracketPerp = perp;
} else {
// is this bracket better as a suffix?
Point2d sp1 = suffixBracket.getFirstPoint();
Point2d sp2 = suffixBracket.getSecondPoint();
double bestMaxX = Math.max(sp1.x, sp2.x);
double thisMaxX = Math.max(p1.x, p2.x);
double bestMaxY = Math.max(sp1.y, sp2.y);
double thisMaxY = Math.max(p1.y, p2.y);
// choose the most eastern or.. the most southern
double xDiff = thisMaxX - bestMaxX;
double yDiff = thisMaxY - bestMaxY;
if (xDiff > EQUIV_THRESHOLD || (xDiff > -EQUIV_THRESHOLD && yDiff < -EQUIV_THRESHOLD)) {
suffixBracket = bracket;
suffixBracketPerp = perp;
}
}
}
// write the labels
if (suffixBracket != null) {
Point2d subSufPnt = suffixBracket.getFirstPoint();
Point2d supSufPnt = suffixBracket.getSecondPoint();
// try to put the subscript on the bottom
double xDiff = subSufPnt.x - supSufPnt.x;
double yDiff = subSufPnt.y - supSufPnt.y;
if (yDiff > EQUIV_THRESHOLD || (yDiff > -EQUIV_THRESHOLD && xDiff > EQUIV_THRESHOLD)) {
Point2d tmpP = subSufPnt;
subSufPnt = supSufPnt;
supSufPnt = tmpP;
}
// subscript/superscript suffix annotation
if (subscriptSuffix != null && !subscriptSuffix.isEmpty()) {
TextOutline subscriptOutline =
leftAlign(
makeText(
subscriptSuffix.toLowerCase(Locale.ROOT),
subSufPnt,
suffixBracketPerp,
labelScale));
result.add(GeneralPath.shapeOf(subscriptOutline.getOutline(), foreground));
}
if (superscriptSuffix != null && !superscriptSuffix.isEmpty()) {
TextOutline superscriptOutline =
leftAlign(
makeText(
superscriptSuffix.toLowerCase(Locale.ROOT),
supSufPnt,
suffixBracketPerp,
labelScale));
result.add(GeneralPath.shapeOf(superscriptOutline.getOutline(), foreground));
}
}
} else if (brackets.size() == 2) {
final Point2d b1p1 = brackets.get(0).getFirstPoint();
final Point2d b1p2 = brackets.get(0).getSecondPoint();
final Point2d b2p1 = brackets.get(1).getFirstPoint();
final Point2d b2p2 = brackets.get(1).getSecondPoint();
final Vector2d b1vec = VecmathUtil.newUnitVector(b1p1, b1p2);
final Vector2d b2vec = VecmathUtil.newUnitVector(b2p1, b2p2);
final Vector2d b1pvec = VecmathUtil.newPerpendicularVector(b1vec);
final Vector2d b2pvec = VecmathUtil.newPerpendicularVector(b2vec);
// Point the vectors at each other
if (b1pvec.dot(VecmathUtil.newUnitVector(b1p1, b2p1)) < 0) b1pvec.negate();
if (b2pvec.dot(VecmathUtil.newUnitVector(b2p1, b1p1)) < 0) b2pvec.negate();
// scale perpendicular vectors by how deep the brackets need to be
b1pvec.scale(bracketDepth);
b2pvec.scale(bracketDepth);
// bad brackets
if (Double.isNaN(b1pvec.x)
|| Double.isNaN(b1pvec.y)
|| Double.isNaN(b2pvec.x)
|| Double.isNaN(b2pvec.y)) return result;
Path2D path = new Path2D.Double();
if (round) {
// bracket 1 (cp: control point)
path.moveTo(b1p1.x + b1pvec.x, b1p1.y + b1pvec.y);
Point2d cpb1 = VecmathUtil.midpoint(b1p1, b1p2);
cpb1.add(VecmathUtil.negate(b1pvec));
path.quadTo(cpb1.x, cpb1.y, b1p2.x + b1pvec.x, b1p2.y + b1pvec.y);
// bracket 2 (cp: control point)
path.moveTo(b2p1.x + b2pvec.x, b2p1.y + b2pvec.y);
Point2d cpb2 = VecmathUtil.midpoint(b2p1, b2p2);
cpb2.add(VecmathUtil.negate(b2pvec));
path.quadTo(cpb2.x, cpb2.y, b2p2.x + b2pvec.x, b2p2.y + b2pvec.y);
} else {
// bracket 1
path.moveTo(b1p1.x + b1pvec.x, b1p1.y + b1pvec.y);
path.lineTo(b1p1.x, b1p1.y);
path.lineTo(b1p2.x, b1p2.y);
path.lineTo(b1p2.x + b1pvec.x, b1p2.y + b1pvec.y);
// bracket 2
path.moveTo(b2p1.x + b2pvec.x, b2p1.y + b2pvec.y);
path.lineTo(b2p1.x, b2p1.y);
path.lineTo(b2p2.x, b2p2.y);
path.lineTo(b2p2.x + b2pvec.x, b2p2.y + b2pvec.y);
}
result.add(GeneralPath.outlineOf(path, stroke, foreground));
// work out where to put the suffix labels (e.g. ht/hh/eu) superscript
// and (e.g. n, xl, c, mix) subscript
// TODO: could be improved
double b1MaxX = Math.max(b1p1.x, b1p2.x);
double b2MaxX = Math.max(b2p1.x, b2p2.x);
double b1MaxY = Math.max(b1p1.y, b1p2.y);
double b2MaxY = Math.max(b2p1.y, b2p2.y);
Point2d subSufPnt = b2p2;
Point2d supSufPnt = b2p1;
Vector2d subpvec = b2pvec;
double bXDiff = b1MaxX - b2MaxX;
double bYDiff = b1MaxY - b2MaxY;
if (bXDiff > EQUIV_THRESHOLD || (bXDiff > -EQUIV_THRESHOLD && bYDiff < -EQUIV_THRESHOLD)) {
subSufPnt = b1p2;
supSufPnt = b1p1;
subpvec = b1pvec;
}
double xDiff = subSufPnt.x - supSufPnt.x;
double yDiff = subSufPnt.y - supSufPnt.y;
if (yDiff > EQUIV_THRESHOLD || (yDiff > -EQUIV_THRESHOLD && xDiff > EQUIV_THRESHOLD)) {
Point2d tmpP = subSufPnt;
subSufPnt = supSufPnt;
supSufPnt = tmpP;
}
// subscript/superscript suffix annotation
if (subscriptSuffix != null && !subscriptSuffix.isEmpty()) {
TextOutline subscriptOutline =
leftAlign(
makeText(subscriptSuffix.toLowerCase(Locale.ROOT), subSufPnt, subpvec, labelScale));
result.add(GeneralPath.shapeOf(subscriptOutline.getOutline(), foreground));
}
if (superscriptSuffix != null && !superscriptSuffix.isEmpty()) {
TextOutline superscriptOutline =
leftAlign(
makeText(
superscriptSuffix.toLowerCase(Locale.ROOT), supSufPnt, subpvec, labelScale));
result.add(GeneralPath.shapeOf(superscriptOutline.getOutline(), foreground));
}
}
return result;
}