Integration between Marvin Sketch and CHEMIA

MarvinSketch allows users to quickly draw molecules through basic functions on the GUI and advanced functionalities such as sprout drawing, customisable shortcuts, abbreviated groups, default and user-defined templates and context-sensitive popup menus.

Chemical structure drawing

Atom and Bond properties

MarvinSketch has a rich support for atom and bond properties. Users can assign stereochemistry, charge, valence, radicals and isotopes to each atom. Single, double, triple bonds and aromatic forms are supported. Moreover, using wedge bonds user can assign stereochemistry to atoms. Additional data fields can also be attached to atoms, via “S-group” logic so that any user-defined information can be stored directly with the structural information.

Reaction drawing

You can draw single step reactions in MarvinSketch by placing a reaction arrow in any position, pointing in any direction in relation to reaction products. The structures ‘in front’ of the arrow will be recognized as reactants, structures ‘above’ the arrow as agents, and structures behind as products. Atoms can be automatically or manually mapped using the arrow function.

Reaction Drawing

Query drawing

Atom lists, bond lists, not lists, generic atoms, R-groups, and lone pairs are among the query building features available in MarvinSketch. Link nodes, repeating units, pseudo atoms and homology groups, S-groups with attached data are also supported. SMARTS rules allow users to define any specific or generic queries.

Query Drawing

 

Marvin features

Rich editing:

  • wide range of file types supported
  • 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)

Chemically aware

  • 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)

Cross platorm delivery

  • Marvin is Java based and so can run on all major operating systems
    • 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
    • Java Web Start enables web delivery of end user applications
  • .NET support

 

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