Hi Scooter,
This is now much easier, for most use-cases you use the new
DepictionGenerator
<http://cdk.github.io/cdk/1.5/docs/api/index.html?org/openscience/cdk/depict/DepictionGenerator.html>
abstract (module cdk-depict will be bundled but needs to be load
separately). Lots of tweaks you can do but it's a one liner:
new DepictionGenerator().depict(rxn).writeTo("~/myrxn.svg");
The web application can show you what it will look like:
http://cdkdepict-openchem.rhcloud.com/depict.html
John
Regards,
John W May
john.wilkinson...@gmail.com
On 5 March 2016 at 04:49, Scooter Morris <scoo...@cgl.ucsf.edu> wrote:
> Hi all,
> I've been trying to add reactions to the chemViz2 plugin for
> Cytoscape and have been unsuccessful so far. I do get the something
> rendered, but everything is on top of each other and much, much larger
> that I think it should be. Here are the steps I'm taking -- any
> direction would be really helpful.
>
> First, I layout the reaction:
>
> static public IReaction layoutReaction(IReaction reaction) throws
> CDKException {
> int offset = -10;
> // Layout agents
> AtomContainerSet agents = new AtomContainerSet();
> for (IAtomContainer agent: reaction.getAgents().atomContainers()) {
> IAtomContainer newAgent = layoutMolecule(agent);
> agents.addAtomContainer(newAgent);
> }
> // ??? no setAgents method ???
> reaction.getAgents().removeAllAtomContainers();
> for (IAtomContainer agent: agents.atomContainers()) {
> reaction.addAgent(agent);
> }
>
> // Layout reactants
> AtomContainerSet reactants = new AtomContainerSet();
> for (IAtomContainer reactant:
> reaction.getReactants().atomContainers()) {
> IAtomContainer newReactant = layoutMolecule(reactant);
> GeometryTools.translate2DCenterTo(newReactant, new
> Point2d(offset, 0));
> offset += 2;
> reactants.addAtomContainer(newReactant);
> }
> reaction.setReactants(reactants);
> // Layout Products
> offset += 6;
> AtomContainerSet products = new AtomContainerSet();
> for (IAtomContainer product: reaction.getProducts().atomContainers())
> {
> IAtomContainer newProduct = layoutMolecule(product);
> GeometryTools.translate2DCenterTo(newProduct, new Point2d(offset,
> 0));
> offset += 2;
> products.addAtomContainer(newProduct);
> }
> reaction.setProducts(products);
> return reaction;
> }
>
> where layoutMolecule is the code I'm already using to layout
> IAtomContainers and seems to work well.
>
> Then, when I actually do the rendering:
>
> ChemModelRenderer renderer = getReactionRenderer((Color)background);
> ChemModel chemModel = new ChemModel();
> ReactionSet rSet = new ReactionSet();
> rSet.addReaction(iReaction);
> chemModel.setReactionSet(rSet);
> if (renderer == null)
> return null;
>
>
> (I tried ReactionRenderer also, but got the same results....)
>
> where getReactionRenderer is:
> private static ChemModelRenderer getReactionRenderer(Color background) {
> // generators make the image elements
> Font font = new Font("Arial", Font.PLAIN, 24);
> ChemModelRenderer renderer =
> new ChemModelRenderer(Arrays.asList(new BasicSceneGenerator(),
> new StandardGenerator(font)),
> Arrays.asList((IGenerator<IReaction>)new ReactionSceneGenerator(),
> (IGenerator<IReaction>)new ReactionArrowGenerator(),
> (IGenerator<IReaction>)new ReactionPlusGenerator()),
> new AWTFontManager());
>
> RendererModel model = renderer.getRenderer2DModel();
> model.set(StandardGenerator.Visibility.class,
> SymbolVisibility.iupacRecommendations());
> model.set(StandardGenerator.AtomColor.class, new CDK2DAtomColors());
> model.set(StandardGenerator.StrokeRatio.class, 0.85);
> model.set(StandardGenerator.SymbolMarginRatio.class, 4d);
>
> if (background == null)
> background = new Color(255,255,255,255);
>
> return renderer;
> }
>
> I seem to be missing a major step here since the result is a mess. Any
> suggestions or direction would be helpful. I'm currently using 1.5.12,
> but I've also tried with 1.5.11 to no avail....
>
> -- scooter
>
>
>
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