AMBER Archive (2006)

Subject: Re: AMBER: Announcement: Amber 9 is now available

From: FyD (fyd_at_u-picardie.fr)
Date: Mon Apr 03 2006 - 13:00:44 CDT

Quoting Feng X Zhou <feng.zhou_at_abbott.com>:

We started to generate CML files http://www.xml-cml.org/ from Tripos mol2 files:
This allows to visualize structure and charge values using Jmol
http://jmol.sourceforge.net/ and Java. This "mol2tocml.pl" perl script will be
available (GPL) from the R.E.D./R.E.DD.B. home page and from the R.E.D.
tutorial home page.

regards, Francois

> Excuse me for my lack of knowledge in this field (I work mostly with
> computers)... and hence this might be a totally irrelevant remark, but
> could XML format be a possible future candidate for Topo, param, or even
> Coordinates?
>
> It would seem like a great simplifier of the parsers (if all config &
> input data is in XML), only one parser would be needed using readily
> available XML libraries and the proram just need to deal with the data
> structures rather than formats, and it is human friendly. XML is not
> disk space efficient but given the amount of disk spaces available these
> days, perhaps this would not be a major concern?
>
> This may not be compatible with the format most people use today, but it
> seems Bioinformatics (sequencing) people are already using XML a lot....
> (for sequence data and homology studies)?
>
> -Feng Zhou

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