MarvinSketch
Related links
Overview
MarvinSketch is an advanced chemical editor for drawing chemical structures, queries and reactions. It has a rich (and growing) list of editing features, is chemically aware and is able to call ChemAxon’s structure based calculation plugins for structures on the canvas.
Rich editing:- wide range of file types supported: MOL, MOL2, SDF, RXN, RDF (V2000/V3000), SMILES, SMARTS/SMIRKS (recursive), MRV, InChi, CML, PDB etc
- Copy and paste between different editors
- Abbreviated groups
- Pre-loaded structure templates and “My Templates”
- 3D editing
- 3D geometry and conformer generation
- 2D cleaning and conformer generation
- Advanced query features (generic atoms and bonds, atom lists/not lists, query properties, pseudo atoms, multiple groups, Link nodes, etc)
- Creating and editing molecule sets (without a database)
- Multipage documents and printing support
- Drawing and formatting shapes, arrows and text boxes
- Structure annotation
- User definable customisable styles (colours, structure representations, etc)
- Structure based calculations can be called directly from MarvinSketch. For a complete listing of functions please see the Calculator Plugins section
- Error checking (valence and reaction error checking)
- Structure query design (R-logic, SMARTS properties, etc)
- Isotopes, charges radicals, lone pairs and aliases are supported
- Manual and automapping for reaction drawing
- Advanced stereochemistry functions (E/Z double bonds, R/S chirality, ABS/OR/AND enhanced stereo, etc)
- Marvin can run on all major operating systems, it is available in the following distributions:
- Java Applets can easily be implemented into Java enabled web pages without the need for the user to install software or plugins
- Java Beans can be directly installed to give standalone desktop applications and can also be used to integrate Marvin into Java based applications
- Java Web Start enables web delivery of end user applications
- .NET package makes it available to integrate Marvin into .NET applications
FAQ
What is MarvinSketch?
MarvinSketch is the molecule drawing tool of Marvin, a chemical structure drawing and visualizing package, including an integrated chemical file format converter. Marvin consists of MarvinSketch, MarvinView (single and multiple structure viewer), MarvinSpace (high performance 3D molecule visualizer) and MolConverter (file format batch-conversion tool).
What is MarvinSketch good for?
Molecule sketches, reactions, queries, graphics can be easily made, exported in various file formats.
Who uses MarvinSketch?
MarvinSketch is used in numerous chemistry related fields: chemists, cheminformaticians, lab assistants, teachers, students.
Do I have to do programming for using Marvin?
No, not necessarily. Marvin has a neat user interface, just install it on your desktop. For server installation or applet usage you need programming.
What kind of additional software is needed?
For the Java version you need Java 1.5 or later (included in installer). For the .Net version (coming with 5.3) you need .Net environment.
What kind of distributions are available from Marvin?
Beans (including a standalone application), applets and JWS
How is Marvin integrated into .Net solutions?
Presently it can be integrated through JNBridge. A pure .Net version is under development and is being released with version 5.3.
What kind of browsers are supported?
We support Internet Explorer, Mozilla Firefox, Chrome, Netscape, Safari and Opera.
I frequently use special tools, and I don’t need some menu items. Can I customize the menu, the toolbar and the shortcuts?
Yes. In addition for those who switch from other software to Marvin, there are predifined configurations where the toolbar icons and the menu options are arranged similar to other chemical sketchers, like ISIS/Draw or ChemDraw.
I have a compound family with a special basic structure that I often use. Can I create my own templates?
Yes. Any structure from the canvas can simply be drag & dropped to the MyTemplates toolbar, and if it was a superatom s-group, it is automatically added to the abbreviated group list. From version 5.3 you can even add a molecule set to the templates in the Template Library dialog window.
Can I edit the structures directly from Word or Powerpoint documents?
Yes, a simple copy/paste inserts a Marvin object into office documents that you can edit afterwards by simply double-clicking the drawing. Marvin uses OLE2 technology making the inline editing of structures in documents possible (i.e. without opening a separate MarvinSketch window).
Is it possible to create transparent images with MarvinSketch?
The images copied into MS Office documents are automatically transparent, and you can also export your sketch to transparent EMF, SVN or PNG format.
Can I edit a molecule in 3D?
Yes, if you have a 3D structure, it still can be edited. If you have a 2D structure, but you would like to see its optimized 3D form, you can use the 3D clean option, and continue the editing in 3D.
