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Correct layout rollback/reset in depiction generator resetting bond t…
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…ypes in addition to the coordinates.
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@johnmay
johnmay committed Jan 5, 2017
1 parent dcfa4d1 commit 72418be
Showing 1 changed file with 52 additions and 36 deletions.
88 changes: 52 additions & 36 deletions app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -337,15 +337,17 @@ public Depiction depict(Iterable<IAtomContainer> mols) throws CDKException {
*/
public Depiction depict(Iterable<IAtomContainer> mols, int nrow, int ncol) throws CDKException {

List<LayoutBackup> layoutBackups = new ArrayList<>();
int molId = 0;
for (IAtomContainer mol : mols) {
setIfMissing(mol, MarkedElement.ID_KEY, "mol" + ++molId);
layoutBackups.add(new LayoutBackup(mol));
}

// ensure we have coordinates, generate them if not
// we also rescale the molecules such that all bond
// lengths are the same.
List<Double> scaleFactors = prepareCoords(mols);
prepareCoords(mols);

// highlight parts
for (Map.Entry<IChemObject, Color> e : highlight.entrySet())
Expand All @@ -361,7 +363,8 @@ public Depiction depict(Iterable<IAtomContainer> mols, int nrow, int ncol) throw
final List<Bounds> molElems = copy.generate(molList, model, 1);

// reset molecule coordinates
resetCoords(mols, scaleFactors);
for (LayoutBackup backup : layoutBackups)
backup.reset();

// generate titles (if enabled)
final List<Bounds> titles = new ArrayList<>();
Expand All @@ -387,37 +390,11 @@ public Depiction depict(Iterable<IAtomContainer> mols, int nrow, int ncol) throw
* @return coordinates
* @throws CDKException
*/
private List<Double> prepareCoords(Iterable<IAtomContainer> mols) throws CDKException {
List<Double> scaleFactors = new ArrayList<>();
private void prepareCoords(Iterable<IAtomContainer> mols) throws CDKException {
for (IAtomContainer mol : mols) {
if (ensure2dLayout(mol)) {
scaleFactors.add(Double.NaN);
} else if (mol.getBondCount() > 0) {
if (!ensure2dLayout(mol) && mol.getBondCount() > 0) {
final double factor = GeometryUtil.getScaleFactor(mol, 1.5);
GeometryUtil.scaleMolecule(mol, factor);
scaleFactors.add(factor);
} else {
scaleFactors.add(1d); // no bonds
}
}
return scaleFactors;
}

/**
* Reset the coordinates to their position before rendering.
*
* @param mols molecules
* @param scales how molecules were scaled
*/
private static void resetCoords(Iterable<IAtomContainer> mols, List<Double> scales) {
Iterator<Double> it = scales.iterator();
for (IAtomContainer mol : mols) {
final double factor = it.next();
if (!Double.isNaN(factor)) {
GeometryUtil.scaleMolecule(mol, 1 / factor);
} else {
for (IAtom atom : mol.atoms())
atom.setPoint2d(null);
}
}
}
Expand All @@ -444,20 +421,24 @@ public Depiction depict(IReaction rxn) throws CDKException {
final List<IAtomContainer> reactants = toList(rxn.getReactants());
final List<IAtomContainer> products = toList(rxn.getProducts());
final List<IAtomContainer> agents = toList(rxn.getAgents());
List<LayoutBackup> layoutBackups = new ArrayList<>();

// set ids for tagging elements
int molId = 0;
for (IAtomContainer mol : reactants) {
setIfMissing(mol, MarkedElement.ID_KEY, "mol" + ++molId);
setIfMissing(mol, MarkedElement.CLASS_KEY, "reactant");
layoutBackups.add(new LayoutBackup(mol));
}
for (IAtomContainer mol : products) {
setIfMissing(mol, MarkedElement.ID_KEY, "mol" + ++molId);
setIfMissing(mol, MarkedElement.CLASS_KEY, "product");
layoutBackups.add(new LayoutBackup(mol));
}
for (IAtomContainer mol : agents) {
setIfMissing(mol, MarkedElement.ID_KEY, "mol" + ++molId);
setIfMissing(mol, MarkedElement.CLASS_KEY, "agent");
layoutBackups.add(new LayoutBackup(mol));
}

final Map<IChemObject, Color> myHighlight = new HashMap<>();
Expand All @@ -468,9 +449,9 @@ public Depiction depict(IReaction rxn) throws CDKException {
myHighlight.putAll(highlight);
highlight.clear();

final List<Double> reactantScales = prepareCoords(reactants);
final List<Double> productScales = prepareCoords(products);
final List<Double> agentScales = prepareCoords(agents);
prepareCoords(reactants);
prepareCoords(products);
prepareCoords(agents);

// highlight parts
for (Map.Entry<IChemObject, Color> e : myHighlight.entrySet())
Expand All @@ -494,9 +475,8 @@ public Depiction depict(IReaction rxn) throws CDKException {
Bounds plus = copy.generatePlusSymbol(scale, fgcol);

// reset the coordinates to how they were before we invoked depict
resetCoords(reactants, reactantScales);
resetCoords(products, productScales);
resetCoords(agents, agentScales);
for (LayoutBackup backup : layoutBackups)
backup.reset();

final Bounds emptyBounds = new Bounds();
final Bounds title = copy.getParameterValue(BasicSceneGenerator.ShowReactionTitle.class) ? copy.generateTitle(rxn, scale) : emptyBounds;
Expand Down Expand Up @@ -1142,4 +1122,40 @@ private static String getDefaultOsFont() {
// TODO: Native Font Support - choose best for Win/Linux/OS X etc
return Font.SANS_SERIF;
}

/**
* Utility class for storing coordinates and bond types and resetting them after use.
*/
private static final class LayoutBackup {
private final Point2d[] coords;
private final IBond.Stereo[] btypes;
private final IAtomContainer mol;

public LayoutBackup(IAtomContainer mol) {
final int numAtoms = mol.getAtomCount();
final int numBonds = mol.getAtomCount();
this.coords = new Point2d[numAtoms];
this.btypes = new IBond.Stereo[numBonds];
this.mol = mol;
for (int i = 0; i < numAtoms; i++) {
IAtom atom = mol.getAtom(i);
coords[i] = atom.getPoint2d();
if (coords[i] != null)
atom.setPoint2d(new Point2d(coords[i])); // copy
}
for (int i = 0; i < numBonds; i++) {
IBond bond = mol.getBond(i);
btypes[i] = bond.getStereo();
}
}

void reset() {
final int numAtoms = mol.getAtomCount();
final int numBonds = mol.getAtomCount();
for (int i = 0; i < numAtoms; i++)
mol.getAtom(i).setPoint2d(coords[i]);
for (int i = 0; i < numBonds; i++)
mol.getBond(i).setStereo(btypes[i]);
}
}
}

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