What is Marvin and how to ...

1. György Pirok, Szilárd Dóránt What is Marvin and how to ... May, 2005

2. Contents Marvin in action Features Various file formats Structure Cleaning Stereo features Templates Abbreviated and multiple groups R-group queries Other sketching goodies Calculator Plugins MarvinView tables Marvin as a building block • Marvin Applets • Applet specific features • Applet – JavaScript communication • MarvinView tables on the web • Marvin Beans • API examples Integration Import / export

3. Marvin in Action

4. Features Sketch molecules • isotopes, charges, radicals, lone pairs • stereo atoms and bonds (R/S, E/Z) • diastereomers (ABS/AND/OR) • alias, pseudo atoms • templates • abbreviated and multiple groups • link nodes • curved arrows • attached data • reactions (automapping) Design queries • generic atoms and bonds • atom lists and not lists • SMARTS expressions (even recursive) • R-groups View compound sets • Table layout • 3D models Compatible • MOL, SDF, RXN, RDF (V2000/V3000) • SMILES, SMARTS/SMIRKS (recursive too) • MRV, CML, PDB • copy/paste Flexible • 2D Cleaning • 3D geometry/conformers • Shapes, text boxes • Calculation Plugins Available • Java applets, signed applets • Applications, deployment with • Installer • Java Web Start • JavaBeans • Java 1.1-1.5 platforms (Windows, Mac, Linux/Unix) • full API • documentation and examples • free for the Academic community

5. Various file formats

6. Structure Cleaning CC(C)NCC(O)COC1=C2C=C(C)NC2=CC=C1 topology 2D 3D

7. Stereo features

8. Templates

9. Abbreviated and multiple groups

10. R-group queries

11. Other sketching goodies curved arrows link nodes attached data 3D sketching

12. Calculator Plugins • ChemAxon’s plugin loading mechanism enables Marvin to provide access to a wide range of dynamically loaded calculation tools • A set of plugins is provided by ChemAxon: pKa, logP, logD, Huckel Analysis, Hydrogen Bond Donor / Acceptor, etc. • Users can easily add their own calculator plugins to this framework

13. MarvinView tables

14. Marvin as a building block

15. Marvin Applets Browser-independent solution for integrating Marvin applets into the HTML source: <script LANGUAGE="JavaScript1.1" SRC="../../marvin.js"></script> <script LANGUAGE="JavaScript1.1"> <!– msketch_begin("../..", 460, 380);// arguments: CODEBASE, WIDTH, HEIGHT msketch_param(“mol", “../structures/benzene.mol”);// structure URL as applet parameter // alternatively the structure source can also be specified: msketch_param(“mol", “c1ccccc1”);// structure source as applet parameter msketch_param(“colorScheme", “cpk”);// applet parameter … msketch_end(); //--> </script>

16. Applet specific features (1) 1. Both Swing and AWT versions are available for maximum compatibility, the appropriate version for the browser / JRE is automatically selected 2. Signed (trusted) applets enable access to local files, system clipboard and allow printing

17. Applet specific features (2) 3. Modularity • Modular loading of packages ensures fast download-time • Modules are not included into the main jar, they are loaded on demand • Preloading of frequently used modules can be specified with applet parameter: msketch_param("preload", "MolExport,Parity,SmilesExport,Clean2D,MyformatExport");

18. Applet – JavaScript communication • The applet API is accessible from JavaScript, providing a convenient solution to • Fetch the current structure from the applet in a specified file format. This is typically used for sending the structure to the server for further processing. • Change the structure or display options of the applet without reloading the page.

19. MarvinView tables on the web “Live” structures in a HTML page with associated data:

20. Marvin Beans • Use Marvin Beans to add MarvinSketch or MarvinView as a graphical component to your standalone application • Additional API is accessible for • Import / Export • Performing calculations with plugins • 2D and 3D cleaning of structures • etc.

21. API example : integration Adding a Marvin Sketch component to a dialog: www.chemaxon.com/marvin/examples/dialog/DialogLauncher.java.txt JDialog dialog = new JDialog(…); MSketchPane sketcher = new MSketchPane(); dialog.getContentPane().add(sketcher); … Molecule mol= sketcher.getMol(); //getting the sketched molecule Adding a Marvin View component to a dialog: JDialog dialog = new JDialog(…); MViewPane viewer = new MViewPane(); Molecule mol = …; viewer.setM(0, mol); //setting a molecule to display dialog.getContentPane().add(viewer); Full java source is available at:

22. API example : import / export Import: String fileName=“sample.mol”; MolImporter importer = new MolImporter(fileName); Molecule mol = importer.read(); Export: String format = … ; byte[] data = mol.toBinFormat(format); // for all formats String output=mol.toFormat(“mol”); //only for text formats Full java source is available at: www.chemaxon.com/marvin/examples/converter/SimpleConverter.java.txt

23. Summary ChemAxon’s MarvinSketch and MarvinView are chemically aware, flexible applications enabling the chemist to draw and display chemical structures and to perform predictive calculations. Marvin Beans and Marvin Applets allow developers to integrate these tools into standalone and web applications with ease.

24. Links • Marvin home page • www.chemaxon.com/marvin • Full Marvin API: • www.chemaxon.com/marvin/doc/api • Animated demos and tutorials • www.chemaxon.com/demosite/marvin • Brochures: • www.chemaxon.com/brochures/MarvinSketch.pdf • www.chemaxon.com/brochures/MarvinView.pdf

25. Máramaros köz 3/a Budapest, 1037Hungaryinfo@chemaxon.comwww.chemaxon.com Thank you for your attention