1. Scientific & technical presentation MarvinSketch and MarvinView
May 2008

2. Instead of Introduction
Why Marvin? Marvin is the paranoid robot from The Hitchhikers Guide to The Galaxy.

3. Technical Features File types to read/write: Flexible
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)

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
Marvin can import/export molecules from/into several chemical file formats.

5. Multirecord file open in MarvinSketch

6. Converting Images to Structure using OSRA

7. Image Export Marvin can generate image from a molecule.
Create raster or vector graphical image from your structure.
Marvin can generate image from a molecule.

8. OLE component for documents
Editable molecules in Office documents
Marvin can generate image from a molecule.

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

10. Distributions / Marvin Beans
Desktop applications (deployment with Java or .NET Installer or Java Web Start)
Full API (with JavaBean or .NET support) 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
Marvin is available in the following distributions.

11. Distributions / Marvin Applets
Browser-independent solution for Marvin integration into web pages
Wide range of layout customization
API to control the applets from JavaScript
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

12. Web Browser Compatibility
Internet Explorer
Firefox
Mozilla
Netscape
Safari
Opera
Marvin applets can run in all Java capable browser.

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
You can specify actions to buttons in the Marvin Applets.

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 of structures
- All operations accessible in the GUIs are also available in the API.
Developing with Marvin Beans

16. Molecule Sketching Features
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
A quick review about Marvin features.

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

18. Stereo Features, Lone Pairs
Marvin can display stereo infos.

19. Reactions
A reaction with agent and atom mappings.

20. Templates
With help of the templates, drawing is more easy.

21. Bold bonds and their juncitons

22. Brackets as graphical objects

23. Abbreviated and Multiple Groups
Abbreviated groups are expandable. You can set theirs status through the menu.

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

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 and General Chemistry Features
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
A quick review about Marvin features.

31. R-group Queries
R-groups support is useful for query drawing.

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

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
By selecting the Edit->Clean->3D- >Select conformer menu option, you can choose among them.

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
Several display options are common in sketcher and in viewer.

39. Further Display Features
In viewer, structures can move.
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
MarvinView application can display property fields of SD files.

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
MarvinView application can display property fields of SD files.

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 other technical presentations
MarvinSketch/View
MarvinSpace
Calculator Plugins
JChem Base
JChem Cartridge
Standardizer
Screen
JKlustor
Fragmenter
Reactor

44. Links Marvin home page Full Marvin API: Animated demos and tutorials
Full Marvin API:
Animated demos and tutorials
Brochures: