bug with arrangeComponents

when using the arrangeComponents() method on a RxnMolecue if there is a group (like NO2) then the molecules end up positioned wrong. Please see sample code below.





import chemaxon.formats.MolImporter;


import chemaxon.struc.RxnMolecule;





import javax.swing.*;


import java.awt.*;





public class MarvinGroups {


public static void main(String[] args) throws Exception {


RxnMolecule orginalRxn = (RxnMolecule) MolImporter.importMol("<?xml version=\"1.0\" ?>\n" +


"<MDocument>\n" +


" <MChemicalStruct>\n" +


" <reaction>\n" +


" <reactantList>\n" +


" <molecule molID=\"m1\">\n" +


" <atomArray\n" +


" atomID=\"a1 a2 a3 a4 a5 a6\"\n" +


" elementType=\"N C C C C R\"\n" +


" sgroupRef=\"0 0 0 0 0 sg1\"\n" +


" x2=\"-15.364680037388974 -16.683703699331744 -16.65493642961884 -13.988121836020401 -14.016889105733304 -17.72334933421448\"\n" +


" y2=\"-0.5901183809130967 0.20465971946152162 1.744391009068011 1.6945660979252635 0.15483480831877428 2.853486976644085\"\n" +


" />\n" +


" <bondArray>\n" +


" <bond atomRefs2=\"a1 a2\" order=\"1\" />\n" +


" <bond atomRefs2=\"a1 a5\" order=\"1\" />\n" +


" <bond atomRefs2=\"a2 a3\" order=\"2\" />\n" +


" <bond atomRefs2=\"a3 a4\" order=\"1\" />\n" +


" <bond atomRefs2=\"a3 a6\" order=\"1\" />\n" +


" <bond atomRefs2=\"a4 a5\" order=\"2\" />\n" +


" </bondArray>\n" +


" <molecule id=\"sg1\" role=\"SuperatomSgroup\" title=\"NO2\"\n" +


" leftName=\"O2N\" molID=\"m2\">\n" +


" <atomArray\n" +


" atomID=\"a7 a8 a9\"\n" +


" elementType=\"N O O\"\n" +


" attachmentPoint=\"1 0 0\"\n" +


" x2=\"-29.69166660308838 -28.15166660308838 -31.231666603088378\"\n" +


" y2=\"15.166666746139526 15.166666746139526 15.166666746139526\"\n" +


" />\n" +


" <bondArray>\n" +


" <bond atomRefs2=\"a8 a7\" order=\"2\" />\n" +


" <bond atomRefs2=\"a7 a9\" order=\"2\" />\n" +


" </bondArray>\n" +


" </molecule>\n" +


" </molecule>\n" +


" </reactantList>\n" +


" <productList>\n" +


" <molecule molID=\"m3\">\n" +


" <atomArray\n" +


" atomID=\"a1 a2 a3 a4 a5 a6\"\n" +


" elementType=\"C C C C C C\"\n" +


" x2=\"9.274999618530273 7.941330277482015 7.941330277482015 9.274999618530273 10.608668959578532 10.608668959578532\"\n" +


" y2=\"2.765033904959939 1.9950169644009002 0.45498308328281745 -0.315033857276223 0.45498308328281745 1.9950169644009002\"\n" +


" />\n" +


" <bondArray>\n" +


" <bond atomRefs2=\"a1 a2\" order=\"1\" />\n" +


" <bond atomRefs2=\"a2 a3\" order=\"2\" />\n" +


" <bond atomRefs2=\"a3 a4\" order=\"1\" />\n" +


" <bond atomRefs2=\"a4 a5\" order=\"2\" />\n" +


" <bond atomRefs2=\"a5 a6\" order=\"1\" />\n" +


" <bond atomRefs2=\"a1 a6\" order=\"2\" />\n" +


" </bondArray>\n" +


" </molecule>\n" +


" </productList>\n" +


" </reaction>\n" +


" </MChemicalStruct>\n" +


"</MDocument>");





RxnMolecule rxn = new RxnMolecule();


for(int i=0; i<orginalRxn.getReactantCount(); i++) {


rxn.addComponent(orginalRxn.getReactant(i).cloneMolecule(), RxnMolecule.REACTANTS);


}





for(int i=0; i<orginalRxn.getProductCount(); i++) {


rxn.addComponent(orginalRxn.getProduct(i).cloneMolecule(), RxnMolecule.PRODUCTS);


}





rxn.arrangeComponents();





JFrame f = new JFrame();


f.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);


f.setLayout(new GridLayout(2, 1));


f.add(new JLabel(new ImageIcon((Image) orginalRxn.toObject("imagew300,h300"))));


f.add(new JLabel(new ImageIcon((Image) rxn.toObject("imagew300,h300"))));


f.pack();


f.setVisible(true);


}


}

It seems that

Code:

MoleculeGraph.arrangeComponents()

does not work properly for Sgroups. We will investigate this problem and let you know when it is fixed.

Do you have any updates on this issue?

We are working on this problem, hopefully, the fix will be available in 4.1.11. Sorry for the delay. We increased the priority of this task.

Hi I just tested this using the new release and while the example provided in the original bug report now works a slightly modified example does not. I have attached an example that still fails.

Hi,





The solution for this problem is to call:

Code:

rxn.setGUIContracted(true);

before transforming the molecule.


I hope this helps. The modified code is attached.





for more explanation, see:


http://www.chemaxon.com/forum/ftopic1423.html&highlight=setguicontracted





Best regards,


Erika

Thanks - that does the trick.





Trevor