From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Feb 08 2008 - 08:03:31 CST

On Fri, 8 Feb 2008, Olaf Lenz wrote:

[...]

OL> Is it also possible to deactivate automatic bond-search for a specific
OL> format in the molfile reader plugin? For VTF files that usually contain
OL> the data of coarse-grained simulations, automatic bond-search is
OL> unwanted and significantly slows down loading of a molecule.

olaf,

bond searching is only performed, if the plugin does not
provide bonding information. if you provide a read_bonds
entry in the molfile plugin structure, then VMD will use
that information instead. just make your plugin recognize
that you don't want read bonds by some marker in the file
and then have your read_bonds function return an empty list

=> no bonds, and no searching.

cheers,
   axel.

ps: the major slowdown for vtf is probably the time spent
on parsing the file. we're routinely using .psf/.dcd or
.psf/.xtc for large CG systems and the reading of the .psf
is painfully slow at times,... and even the decoding time
for compressed .xtc becomes an issue for long trajectories.

OL>
OL> Olaf
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-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.