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Chemical editor: summary

Chemical editor: summary. Based on the requirements and user needs, the chemical editor/chopper should: Display atom labels Allow selection of atoms/bonds Provide integrated edit views: chemical diagram, tabular editor, 3-D. Of the shelf components. Jmol applet - ChemAxon sketch editor

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Chemical editor: summary

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  1. Chemical editor: summary Based on the requirements and user needs, the chemical editor/chopper should: • Display atom labels • Allow selection of atoms/bonds • Provide integrated edit views: chemical diagram, tabular editor, 3-D

  2. Of the shelf components • Jmol applet - ChemAxon sketch editor Requirements: • Jmol needs standard java 1.4 but ChemAxon uses advanced applet features (is a singed applet – loads many libraries on the background) • Integration of ChemAxon within a web-page is often problematic (security warnings - browser crashes etc)

  3. Other problems with ChemAxon • It is a closed – black-box type of applet • It does not retain atom label information • The annotators will have to figure out where atoms are, by constantly matching the diagram with the 3-D view. This is not easy and error prone for large/symmetric molecules • There is big information loss in the ChemAxon output – there is not a reliable way to figure out what the user did • There is not way to process user interaction events like selecting atoms/bonds

  4. Options • Use these components but implement a user unfriendly editor with unpredictable behavior • Not use a chemical diagram editor at all and use only 3D viewer. It will not be possible to perform integrated edit operations (adding leaving atoms – change names etc) • Implement a new component – Options: • Java applet • HTML native

  5. Applets • Pros: • We use applets for other functions Cons: • Java interaction with HTML is problematic • External users have different java engines, or not have java at all - there are often problems with security exceptions • A Java implementation is a lot more complicated

  6. HTML Canvas • Pros • Tighter integration with HTML and Ajax technologies • A lot simpler coding model • No need or sensitive to user java engines Cons • Not a strong standard yet. Internet explorer is supported via additional library (excanvas). Performance on I.E. is not as good

  7. My opinion: HTML canvas • Easy integration in HTML. It would not be possible to reliably link 2 applets in an HTML page (diagram editor – jmol) • A lot faster to implement (maybe 3 times faster) • A java front-end solution of this size would be more suitable as a standalone application rather than a web based tool.

  8. Current state of prototype • A lot of functionality is there but there are still many bugs • Has been tested and works on: • Firefox 3 (3.5 on mac 3.6 on win7) • Internet explorer 8 – in normal and compatibility mode • Internet explorer 6 • Safari 4.0 on win7 and 5.0 on mac • Chrome 5.0 on win7 and mac

  9. Urls • Integrated views with load ability http://biolit2.rcsb.org/doc/images/d_a/chemDiagram.html • Standalone diagram editor: http://biolit2.rcsb.org/doc/images/d_a/chemEdit.html • Integration of diagram editor, tabular editor, 3-D view: http://biolit2.rcsb.org/doc/images/d_a/chemViews.html

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