What is Marvin and how to ...
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György Pirok, Szilárd Dóránt
May, 2005
What is Marvin and how to ...
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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
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Slide 3
Marvin Applets and Marvin Beans — May 2005
Marvin in Action
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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 1.1-1.5 platforms (Windows, Mac,
Linux/Unix)– full API– documentation and examples– free for the Academic community
Features
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Slide 5
Marvin Applets and Marvin Beans — May 2005
Various file formats
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CC(C)NCC(O)COC1=C2C=C(C)NC2=CC=C1
3D2D
topology
Structure Cleaning
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Slide 7
Marvin Applets and Marvin Beans — May 2005
Stereo features
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Marvin Applets and Marvin Beans — May 2005
Templates
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Marvin Applets and Marvin Beans — May 2005
Abbreviated and multiple groups
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Slide 10
Marvin Applets and Marvin Beans — May 2005
R-group queries
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Marvin Applets and Marvin Beans — May 2005
curved arrows
attached data
link nodes
3D sketching
Other sketching goodies
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Marvin Applets and Marvin Beans — May 2005
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
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Slide 13
Marvin Applets and Marvin Beans — May 2005
MarvinView tables
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Slide 14
Marvin Applets and Marvin Beans — May 2005
Marvin as a building block
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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>
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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
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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");
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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.
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Marvin Applets and Marvin Beans — May 2005
MarvinView tables on the web
“Live” structures in a HTML page with associated data:
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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.
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API example : integration
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 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 displaydialog.getContentPane().add(viewer);
Full java source is available at:
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API example : import / export
www.chemaxon.com/marvin/examples/converter/SimpleConverter.java.txt
String fileName=“sample.mol”;MolImporter importer = new MolImporter(fileName);Molecule mol = importer.read();
Import:
Export:
String format = … ; byte[] data = mol.toBinFormat(format); // for all formatsString output=mol.toFormat(“mol”); //only for text formats
Full java source is available at:
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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.
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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
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Máramaros köz 3/a Budapest, 1037Hungary
www.chemaxon.com
Thank you for your attention