Chemical editor summary
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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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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

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)


Other problems with chemaxon

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


Options

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


Applets

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


Html canvas

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


My opinion html canvas

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.


Current state of prototype

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


Chemical editor summary

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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