VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 15 2009 - 09:52:21 CDT

Rob,
  If you can send me some test files, I would be happy to test your
code on both big- and little-endian machines to verify it can
read the binary DEN files with either endianism, etc.
If your code doesn't explicitly handle endianism yet, it shouldn't
be too difficult to add.

If the test files are small enough, just gzip and email them to me, otherwise
put them into the VMD Public project on biocore if they're too large.

Also, let me know if you're interested in having this included in VMD 1.8.7.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Jun 14, 2009 at 11:32:28PM -0700, Rob wrote:
>
> Hi,
>
> I have created a plugin for reading two types of output files from ABINIT:
> the formatted/ascii GEO files, and the unformatted/binary DEN files.
> I might put some more work in it later to extend it to other ABINIT in/output files.
>
> Tell me what you think of it, if you are an ABINIT user and want to
> try it out. Source code is here:
>
> http://skku.homeip.net/~lahaye/abinit/abinitplugin.c
>
> All you have to do is:
>
> $ gcc -O2 -Wall -I. -I$VMDBASEDIR/plugins/include -c abinitplugin.c
>
> $ ld -shared -o abinitplugin.so abinitplugin.o
>
> Then
> copy abinitplugin.so $VMDBASEDIR/plugins/$ARCH/molfile
>
> The DEN files contain both structure and volumetric data and therefore
> I read both of them; so after reading the DEN file you have the structure
> plus the density together.
>
> I have tested it on my own Linux systems (Fedora 10 & 11), on which I also
> run the ABINIT code. I'm not sure how machine-independent my code is
> for reading the binary DEN files.Let me know if you encounter problems.
>
> Rob.
>
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078