June, 2007 David Spender*, Erika Biró What's new in Marvin and development discussion.
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Transcript of June, 2007 David Spender*, Erika Biró What's new in Marvin and development discussion.
![Page 1: June, 2007 David Spender*, Erika Biró What's new in Marvin and development discussion.](https://reader033.fdocuments.us/reader033/viewer/2022061306/551465335503462d4e8b5b06/html5/thumbnails/1.jpg)
June, 2007
David Spender*, Erika Biró
What's new in Marvin and development discussion
![Page 2: June, 2007 David Spender*, Erika Biró What's new in Marvin and development discussion.](https://reader033.fdocuments.us/reader033/viewer/2022061306/551465335503462d4e8b5b06/html5/thumbnails/2.jpg)
Contents
What’s new in Marvin?• Structure representation• Better quality graphics• Improved usability• New GUI design• Plug-ins• File IO• Future plans and discussion
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Structure representation• Improvements in Markush
compound drawing (alpha)– Position variation– Repeating unit with repetition ranges
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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
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Structure representation
– Ferrocene, metallocene examples:
Click here for movie
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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
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• Drawing of ordered and unordered mixtures (release 4.1.2)
Structure representation
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Structure representation
• Multistep reaction drawing (alpha)– Reaction scheme with any number and
layout of graphical reaction arrows
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• Left and right abbreviations for abbreviated groups (release 4.1)
Better quality graphics
Click here for movie
![Page 10: June, 2007 David Spender*, Erika Biró What's new in Marvin and development discussion.](https://reader033.fdocuments.us/reader033/viewer/2022061306/551465335503462d4e8b5b06/html5/thumbnails/10.jpg)
Better quality graphics
• Improved 2D cleaning (alpha)– Nice cleaning of big rings (built up
from hexagons) – Template based
Old New
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Better quality graphics
Old New
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Better quality graphics
• New graphical objects – Graphical arrow in reaction (release 4.1.8)
– Graphical brackets (alpha)
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Improved usability
• Status bar with 2D/3D drawing mode selection and modified status (alpha)
• Chain drawing mode button (alpha)
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Improved usability• Insertable OLE component into
MSOffice documents (alpha)
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New GUI design
• Customizable menus and toolbar (alpha)
• Customizable shortcut keys (alpha)
Three ways of customization (alpha) : – Interactive– Configuration file– API
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New GUI design
• Toolbar and menubar icons• Cross-platform “Java Look”
(JGoodies)• Improved User Interface design
and usability “Java Feel” (coming soon)
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New GUI designSample default
layout demonstrating graphics design
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New GUI designCustomization...
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New GUI design
Toolbar icon sizes are
customized
Appearing actions are customized
Menu is reorganized by creating a new custom menu
Sample customized layout
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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)
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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
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Plug-ins– Name generation is free when
used from Marvin GUI. – Real-time updated name display in
MarvinSketch (alpha)
Click here for movie
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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)
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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
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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.