Scientific & technical presentation Marvin Sketch and MarvinView

1. Scientific & technical presentationMarvinSketch and MarvinView May2008

2. Instead of Introduction

3. File types to read/write: MRV, CDX, SKC MOL, SDF, RXN, RDF (V2000/V3000) SMILES, SMARTS/SMIRKS (recursive) XML based format MRV, CML, InChi, MOL2, XYZ, Gaussian Cube PDB, 1 and 3 letter peptide IUPAC and traditional name Flexible Customizable menu/toolbar Custom templates Calculation plugins Custom formatting Image export into BMP, JPEG, PNG, PPM, POV, SVG, EMF, PDF Printing, multipage documents 3D models, Java or OpenGL rendering (with MarvinSpace) Available as Java (signed) applets Applications, deployment with installer, Java Web Start JavaBeans System Requirements: Java 1.5 (or later version) platforms (Windows, Mac, Solaris, Linux/Unix) or .NET (Windows) Technical Features

4. Various File Formats • Molecule source file can be edited and saved or imported/exported in different formats • Possible to insert into a long file of many compounds at a given location • Also possible to read a structure from a given position of a long file • Append current structure to an existing file ChemAxon Marvin Documents | CML | CDX CDXML | SKC | MDL Molfile Extended Molfile Rxnfile Extended Rxnfile RDfile SDfile | Peptide sequence | IUPAC InChI IUPAC Name | SMILES SMARTS | Tripos SYBYL molfile Mol2 | Gaussian Cube | PDB | XYZ

5. Multirecord file open in MarvinSketch

6. Converting Images to Structure using OSRA

7. Image Export • Create raster or vector graphical image from your structure.

8. OLE component for documents • Editable molecules in Office documents

9. System Compatibility • 100% pure Java • .NET integration • Through JNBridge • Windows • 95, 98, Me, NT, 2000, XP, Vista • Mac OS X • Unix/Linux • Linux, Solaris, etc.

10. Marvin Beans Desktopapplications(deployment with Java or .NET Installer or Java Web Start) Full API (with JavaBean or .NETsupport) for developers to use Marvin components in applications Documentation and examples Recommended for end-users Easy installation Support Java 1.5 or .NET capable platforms (Windows, Mac OS X, Linux/Unix) Command line molecule converter Applications are free for end-users Recommended for developers Quick GUI building Easy customization Direct manipulation of molecules Free for open access, non commercial websites Free for academic research and teaching Free for Evaluation Distributions / Marvin Beans

11. Marvin Applets Browser-independent solution for Marvin integration into web pages Wide range of layout customization API to control the applets fromJavaScript Documentation and examples For web developers Simple web base deployment Modular architecture ensures short download time Minimum requirement (Java 1.5 capable browsers) Free for open access, non commercial websites Free for academic research and teaching Free for Evaluation Distributions / Marvin Applets

12. Web Browser Compatibility • Internet Explorer • Firefox • Mozilla • Netscape • Safari • Opera

13. Applet Specific Features • Using Swing GUI components, the appropriate version for the browser / JRE is automatically selected • Signed (trusted) applets enable access to local files, system clipboard and allow printing. • Applet API accessible from JavaScript to • fetch the current structure from the applet and send it to the server for further processing. • change the structure or display options of the applet without reloading the page.

14. Custom Marvin Applets Layout

15. Developing with 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 ofstructures - All operations accessible in the GUIs are also available in the API.

16. Easy sketching Click-drawing, sprout Templates, aliases, pseudo atoms Toolbars, shortcuts Stereo features: tetrahedral (R/S) double bond (E/Z) diastereomer (Abs/And/Not) Reaction (Inv/Ret) Groups Abbreviated, multiple, repeating unit, generic,polymer related groups On-the-fly expanding Bold bonds for projected drawing Bracket objects for Sgroups Attached data Textboxes Graphic objects (arrows, boxes, ellipses, brackets) Curved electron arrows Multi-page layout Rich compound format: Fonts, colors, bond thickness Journal drawing styles to load/save 3D sketching Molecule Sketching Features

17. Click-drawing, sprout, on-the-fly expansion

18. Stereo Features, Lone Pairs

19. Reactions

20. Templates

21. Bold bonds and their juncitons

22. Brackets as graphical objects

23. Abbreviated and Multiple Groups

24. electron flow arrows link nodes attached data 3D sketching Other Sketching Goodies

25. Rich formatting

26. Configuration setting ChemDraw configuration ISIS/Draw configuration

27. Formatting, customizing

28. Customizing drawings • Add graphic objects (lines, arrows, boxes, text boxes) • Possible to change font, color, wire thickness • Save/load different publication styles • Multi-paged documents

29. MarvinSpace Integration • Properties calculated by plugins can be visualized using MarvinSpace

30. Query design features Generic atoms, generic bonds Atom lists/not lists Query properties: hydrogen count, connection count, number of explicit connections, ring count, smallest ring size, ring bond count, substitution count, unsaturation, aromatic/aliphatic atom Topology (ring/chain) Reacting center R-group queries R-logic Position variation Link node Recursive SMARTS Basic chemistry functions: Automatic valence check Automatic lone pair calculation Automatic stereo configuration (R/S, E/Z) Automatic reaction component identification Automatic reaction mapping Conversion between aromatic and Kekulé form Cleaning 2D layout 3D geometry optimizationn Structure checker Automatic error checking Optional fixes for errors Searching in online databases ChemSpider exact search Query and General Chemistry Features

31. R-group Queries

32. Cleaning Options • 2D • optional optimization • wedge bonds cleaning • 3D • fast clean • find low energy conformer • optional hydrogenization • optional optimization • generate conformers CC(C)NCC(O)COC1=C2C=C(C)NC2=CC=C1 Structure Cleaning topology 3D 2D

33. Display Conformers • Using the conformers plugin one can generate the most likely 3D structures and select a suitable one • The corresponding energies are also calculated for a given conformation

34. Structure checker in MarvinSketch GUI

35. Direct search in ChemSpider

36. Advanced (plugin based) Functions • Elemental Analysis • IUPAC Name • Protonation (pKa, Major Microspecies, Isoelectric Point) • Partitioning (logP, logD) • Charge (Charge, Polarizability, Orbital Electronegativity) • Isomers (Tautomers, Resonance, Stereoisomers) • Conformation (Conformers, Molecular Dynamics) • Geometry (Topology analysis, Geometry, Polar surface area (2D), Molecular Surface Area (3D)) • Markush Enumeration • Other (H-bond donor/acceptor, Huckel Analysis, Refractivity)

37. 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 already provided by ChemAxon for a separate license key (single trial is included in every distributions for plugins) • Users can easily add their own calculator plugins to this framework

38. 2D & 3D Structure Visualization • Accurate representation • Rich visualization options • Various display modes (wireframe, ball&stick, spacefill, etc.) • Enable/disable hydrogen visibility (explicit / implicit, on hetero and/or terminal) • Optional display of stereo information • Various rotation modes • Optional valence and reaction error highlighting in sketcher

39. Further Display Features • Single structure or table views • Animated views in viewer

40. Molecule Matrix View • Display SD files with property fields • (Re)customize table layout: visible rows and columns; font size • (Re)scale molecules in cells separately or uniformly

41. Spreadsheet View • Display structures and data field in the same row • Resizable and movable columns • Search and edit in data fields • Fast loading and scrolling of huge SDFiles

42. Summary ChemAxon 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.

43. Visit othertechnical presentations MarvinSketch/Viewhttp://www.chemaxon.com/MarvinSketch_View.ppt MarvinSpacehttp://www.chemaxon.com/MarvinSpace.ppt Calculator Pluginshttp://www.chemaxon.com/Calculator_Plugins.ppt JChem Basehttp://www.chemaxon.com/JChem_Base.ppt JChem Cartridgehttp://www.chemaxon.com/JChem_Cartridge.ppt Standardizerhttp://www.chemaxon.com/Standardizer.ppt Screenhttp://www.chemaxon.com/Screen.ppt JKlustorhttp://www.chemaxon.com/JKlustor.ppt Fragmenterhttp://www.chemaxon.com/Fragmenter.ppt Reactor http://www.chemaxon.com/Reactor.ppt

44. 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