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June , 200 7

What's new in Marvin and development discussion. David Spender*, Erika Bir ó. June , 200 7. Contents. What’s new in Marvin? Structure representation Better quality graphics Improved usability New GUI design Plug-ins File IO Future plans and discussion. Structure representation.

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June , 200 7

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  1. What's new in Marvin and development discussion David Spender*, Erika Biró June, 2007

  2. Contents What’s new in Marvin? • Structure representation • Better quality graphics • Improved usability • New GUI design • Plug-ins • File IO • Future plans and discussion

  3. Structure representation • Improvements in Markush compound drawing (alpha) • Position variation • Repeating unit with repetition ranges

  4. Structure representation • Coordination compounds (alpha) • New bond type: coordinate bond • Between atom – atom: • Between atom – group of atoms: • Connection to a group of atoms with multicenter attachment point Click here for movie

  5. Structure representation • Ferrocene, metallocene examples: Click here for movie

  6. Structure representation • Polymer drawing (alpha) • Source and structure-based representation of polymer types: SRU, repeating unit with repetition ranges, anypolymer, copolymer, crosslink, graft, mer, modification, monomer

  7. Structure representation • Drawing of ordered and unordered mixtures (release 4.1.2)

  8. Structure representation • Multistep reaction drawing (alpha) • Reaction scheme with any number and layout of graphical reaction arrows

  9. Better quality graphics • Left and right abbreviations for abbreviated groups (release 4.1) Click here for movie

  10. Better quality graphics • Improved 2D cleaning (alpha) • Nice cleaning of big rings (built up from hexagons) • Template based Old New

  11. Better quality graphics Old New

  12. Better quality graphics • New graphical objects • Graphical arrow in reaction (release 4.1.8) • Graphical brackets (alpha)

  13. Improved usability • Status bar with 2D/3D drawing mode selection and modified status (alpha) • Chain drawing mode button (alpha)

  14. Improved usability • Insertable OLE component into MSOffice documents (alpha)

  15. New GUI design • Customizable menus and toolbar (alpha) • Customizable shortcut keys (alpha) Three ways of customization (alpha) : • Interactive • Configuration file • API

  16. New GUI design • Toolbar and menubar icons • Cross-platform “Java Look” (JGoodies) • Improved User Interface design and usability “Java Feel” (coming soon)

  17. New GUI design Sample default layout demonstrating graphics design

  18. New GUI design Customization...

  19. New GUI design Sample customized layout Appearing actions are customized Toolbar icon sizes are customized Menu is reorganized by creating a new custom menu

  20. Plug-ins • Tautomerization Calculator Plugin: • Generation of the major (dominant) tautomeric forms based on predicted pKa values. (release 4.1) • Generation of the canonic tautomeric form based on predicted pKa and an empirical rule system.  Filtering of tautomer couples. (release 4.1.9) • Prediction of the tautomer distribution. (release 4.1.9)

  21. Plug-ins • The length of the tautomerization path can optionally be adjusted. (release 4.1.9) • Takes into account the major tautomeric form in the pKa, logP, and the logD calculations. (release 4.2) • Markush enumeration Calculator Plugin (alpha) • Structure to name Calculator Plugin (release 4.1.7) • Traditional or IUPAC name

  22. Plug-ins • Name generation is free when used from Marvin GUI. • Real-time updated name display in MarvinSketch (alpha) Click here for movie

  23. File IO • Saving of specific Marvin settings, stored in mrv with structure (alpha) • PDB import improvements, for example multi-model proteins (release 4.1.2)

  24. Future plans and discussion • Basic structural IO of CDX (ChemDraw) format • Align & distribute for molecules in MarvinSketch • Load Templates from specified directories • Spreadsheet-like table where different columns store different types of data

  25. Future plans and discussion • Name to structure • New skins for Marvin to help chemists who are used to other programs like ChemDraw and Isis/Draw.

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