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

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.