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Step-by-step code examples

Create a JFrame containing a MarvinSpace canvas

Let's create a simple MarvinSpace application.

First, we have to install the Jogl native libraries. MSpaceInstaller will do this for us.

The second step is creating a JFrame.

Third, we have to put the MarvinSpace canvas on it. MSpaceEasy makes it simple, we can also add several GUI components such as Popup Menu and MenuBar.

Finally the frame is ready:

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public void createSimpleMarvinSpaceFrame() throws Exception {

 //parameter true tells that dynamic loading of the Jogl native libraries is necessary

 final chemaxon.marvin.space.MSpaceEasy mspace = new chemaxon.marvin.space.MSpaceEasy(true);



 JFrame frame = new JFrame();

 frame.setTitle(chemaxon.marvin.space.gui.MSpace.programName+" "+chemaxon.marvin.space.gui.MSpace.version);

 frame.setSize(800, 750);

 frame.setLocationRelativeTo(null);

 frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);



 mspace.addCanvas(frame.getContentPane());

 mspace.addPopupMenu();

 mspace.addMenuBar(frame);

 mspace.setSize(600, 600);



 frame.pack();

 frame.show();

}

Load a molecule

To go one step further, we will need some molecules to display. The following code lines can be placed for example before the frame.pack()call.

In case of having a SMILES String:

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 final String molS = "C1C2=CC=CC=C2C3=C4CC5=CC=CC=C5C4=C6CC7=CC=CC=C7C6=C13";

 Molecule mol = MolImporter.importMol(molS);

 mspace.addMolecule( mol );

By default MarvinSpace checks whether the molecule is defined in plane or not, and calls Clean, Hydrogenize and Aromatize functions of the Molecule .

Loading from a file or URL:

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 mspace.addMolecule("http://www.chemaxon.com/MarvinSpace/data/1AID.pdb");

Let's suppose we have a properly initilaized Vector containing Molecule objects. We can place them in different cells each:

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 for(int i=0; i<molVector.size(); i++) {

 mspace.addMoleculeToEmptyCell(molVector.get(i));

 }

Loading a molecule without calling Clean, Hydrogenize and Aromatize:

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 mspace.addMoleculeWithoutChange( mol );

In the previous examples we added the molecules to the scene, but we can also load a molecule by closing all molecules before:

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 mspace.openMolecule( mol );

Loading molecule to a specific cell (indexing starts from 0, from top to bottom and left to right):

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 mspace.addMoleculeTo( mol, 1 );

.