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

2 Slide 2 Marvin Applets and Marvin Beans May 2005 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 Slide 3 Marvin Applets and Marvin Beans May 2005 Marvin in Action

4 Slide 4 Marvin Applets and Marvin Beans May 2005 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 platforms (Windows, Mac, Linux/Unix) –full API –documentation and examples –free for the Academic community Features

5 Slide 5 Marvin Applets and Marvin Beans May 2005 Various file formats

6 Slide 6 Marvin Applets and Marvin Beans May 2005 CC(C)NCC(O)COC1=C2C=C(C)NC2=CC=C1 3D2D topology Structure Cleaning

7 Slide 7 Marvin Applets and Marvin Beans May 2005 Stereo features

8 Slide 8 Marvin Applets and Marvin Beans May 2005 Templates

9 Slide 9 Marvin Applets and Marvin Beans May 2005 Abbreviated and multiple groups

10 Slide 10 Marvin Applets and Marvin Beans May 2005 R-group queries

11 Slide 11 Marvin Applets and Marvin Beans May 2005 curved arrows attached data link nodes 3D sketching Other sketching goodies

12 Slide 12 Marvin Applets and Marvin Beans May 2005 Calculator Plugins ChemAxons 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 Slide 13 Marvin Applets and Marvin Beans May 2005 MarvinView tables

14 Slide 14 Marvin Applets and Marvin Beans May 2005 Marvin as a building block

15 Slide 15 Marvin Applets and Marvin Beans May 2005 Marvin Applets Browser-independent solution for integrating Marvin applets into the HTML source: <!– 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(); //-->

16 Slide 16 Marvin Applets and Marvin Beans May 2005 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 Slide 17 Marvin Applets and Marvin Beans May 2005 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 Slide 18 Marvin Applets and Marvin Beans May 2005 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 Slide 19 Marvin Applets and Marvin Beans May 2005 MarvinView tables on the web Live structures in a HTML page with associated data:

20 Slide 20 Marvin Applets and Marvin Beans May 2005 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 Slide 21 Marvin Applets and Marvin Beans May 2005 API example : integration JDialog dialog = new JDialog(…); MSketchPane sketcher = new MSketchPane(); dialog.getContentPane().add(sketcher); … Molecule mol= sketcher.getMol(); //getting the sketched molecule Adding a Marvin Sketch component to a dialog: 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 Slide 22 Marvin Applets and Marvin Beans May 2005 API example : import / export String fileName=sample.mol; MolImporter importer = new MolImporter(fileName); Molecule mol = importer.read(); Import: 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:

23 Slide 23 Marvin Applets and Marvin Beans May 2005 Summary ChemAxons 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 Slide 24 Marvin Applets and Marvin Beans May 2005 Links Marvin home page – Full Marvin API: – Animated demos and tutorials – Brochures: – –

25 Slide 25 Marvin Applets and Marvin Beans May 2005 Máramaros köz 3/a Budapest, 1037 Hungary Thank you for your attention