Download - June , 200 7
June, 2007
David Spender*, Erika Biró
What's new in Marvin and development discussion
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• Improvements in Markush
compound drawing (alpha)– Position variation– Repeating unit with repetition ranges
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 representation
– Ferrocene, metallocene examples:
Click here for movie
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
• Drawing of ordered and unordered mixtures (release 4.1.2)
Structure representation
Structure representation
• Multistep reaction drawing (alpha)– Reaction scheme with any number and
layout of graphical reaction arrows
• Left and right abbreviations for abbreviated groups (release 4.1)
Better quality graphics
Click here for movie
Better quality graphics
• Improved 2D cleaning (alpha)– Nice cleaning of big rings (built up
from hexagons) – Template based
Old New
Better quality graphics
Old New
Better quality graphics
• New graphical objects – Graphical arrow in reaction (release 4.1.8)
– Graphical brackets (alpha)
Improved usability
• Status bar with 2D/3D drawing mode selection and modified status (alpha)
• Chain drawing mode button (alpha)
Improved usability• Insertable OLE component into
MSOffice documents (alpha)
New GUI design
• Customizable menus and toolbar (alpha)
• Customizable shortcut keys (alpha)
Three ways of customization (alpha) : – Interactive– Configuration file– API
New GUI design
• Toolbar and menubar icons• Cross-platform “Java Look”
(JGoodies)• Improved User Interface design
and usability “Java Feel” (coming soon)
New GUI designSample default
layout demonstrating graphics design
New GUI designCustomization...
New GUI design
Toolbar icon sizes are
customized
Appearing actions are customized
Menu is reorganized by creating a new custom menu
Sample customized layout
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-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-ins– Name generation is free when
used from Marvin GUI. – Real-time updated name display in
MarvinSketch (alpha)
Click here for movie
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
• 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 discussion
• Name to structure• New skins for Marvin to help
chemists who are used to other programs like ChemDraw and Isis/Draw.