1 György Pirok, Szilárd Dóránt May, 2005 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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Marvin in Action

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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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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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Stereo features

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Templates

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Abbreviated and multiple groups

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R-group queries

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curved arrows

attached data

link nodes

3D sketching

Other sketching goodies

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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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MarvinView tables

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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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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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MarvinView tables on the web

“Live” structures in a HTML page with associated data:

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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

info@chemaxon.com

www.chemaxon.com

Thank you for your attention