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Scientific & technical presentation MarvinSketch and MarvinView

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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:

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