AMBER Archive (2006)

Subject: Re: AMBER: Using XML for Amber files

From: Feng X Zhou (
Date: Tue Apr 25 2006 - 10:07:39 CDT

I think it is a great idea -

This would be an approach that could be made even better though - since
the data structure read in from XML might be usable directly in
computation, but this is probably not feasible in short term, since it
requires careful consideration of data structure & changes in computing
code also. Not knowing how AMBER is written, this may or may not be
possible. But if it is written in object oriented languages, it might be
easier in the longer term.

Any way , thanks for consideration of suggestion of a non-biologist.....
And good luck on folding the first protein (someday, from scratch -:)

- Feng Zhou
Worldwide Infrastructure & Networks
Unix/VMS Computer Services
Phone: (847)937-8376

"Xuebin Qiao" <>
Sent by:
04/24/2006 10:57 PM
Please respond to amber

        cc: (bcc: Feng X Zhou/LAKE/CHMS/CONTRACTOR)
        Subject: Re: AMBER: Using XML for Amber files

Dear Feng:

I think a viable practice of XML for amber now is to write library code
for GUI and keep currently computation codes untouched. All we need is to
introduce a temporary adaptor layer that convert XML parameter file into
plain text file and vice versa. GUI use XML files and computation codes
use plain parameter files. When XML get wide accepted, this layer could be
simply discarded then.


... there have been two really clean, 
consistent models of programming so far: 
the C model and the Lisp model. 
These two seem points of high ground, 
with swampy lowlands between them. 

--Paul Graham

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