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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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slide1

What\'s new in Marvin and development discussion

David Spender*, Erika Biró

June, 2007

contents
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
Structure representation
  • Improvements in Markush compound drawing (alpha)
    • Position variation
    • Repeating unit with repetition ranges
structure representation1
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

structure representation2
Structure representation
  • Ferrocene, metallocene examples:

Click here for movie

structure representation3
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
structure representation4
Structure representation
  • Drawing of ordered and unordered mixtures (release 4.1.2)
structure representation5
Structure representation
  • Multistep reaction drawing (alpha)
    • Reaction scheme with any number and layout of graphical reaction arrows
better quality graphics
Better quality graphics
  • Left and right abbreviations for abbreviated groups (release 4.1)

Click here for movie

better quality graphics1
Better quality graphics
  • Improved 2D cleaning (alpha)
    • Nice cleaning of big rings (built up from hexagons)
    • Template based

Old

New

better quality graphics3
Better quality graphics
  • New graphical objects
    • Graphical arrow in reaction (release 4.1.8)
    • Graphical brackets (alpha)
improved usability
Improved usability
  • Status bar with 2D/3D drawing mode selection and modified status (alpha)
  • Chain drawing mode button (alpha)
improved usability1
Improved usability
  • Insertable OLE component into MSOffice documents (alpha)
new gui design
New GUI design
  • Customizable menus and toolbar (alpha)
  • Customizable shortcut keys (alpha)

Three ways of customization (alpha) :

    • Interactive
    • Configuration file
    • API
new gui design1
New GUI design
  • Toolbar and menubar icons
  • Cross-platform “Java Look” (JGoodies)
  • Improved User Interface design and usability “Java Feel” (coming soon)
new gui design2
New GUI design

Sample default layout demonstrating graphics design

new gui design3
New GUI design

Customization...

new gui design4
New GUI design

Sample customized layout

Appearing actions are customized

Toolbar icon sizes are customized

Menu is reorganized by creating a new custom menu

plug ins
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)
plug ins1
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
plug ins2
Plug-ins
  • Name generation is free when used from Marvin GUI.
  • Real-time updated name display in MarvinSketch (alpha)

Click here for movie

file io
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)
future plans and discussion
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
future plans and discussion1
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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