[Jmol-developers] [ jmol-Feature Requests-1002202 ] Tinker format

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Feature Requests item #1002202, was opened at 2004-08-02 21:45
Message generated for change (Comment added) made by nicove
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Category: New IO Format
Group: v10
Status: Open
Priority: 5
Submitted By: Nico (nicove)
Assigned to: Nobody/Anonymous (nobody)
Summary: Tinker format

Initial Comment:
Is it possible to add the reading of the Tinker format ?
The home site of Tinker is http://dasher.wustl.edu/tinker/

If it can help, I'm willing to help as developper to add 
this feature.

Description :
SAMPLE.XYZ

The .xyz file is the basic TINKER Cartesian coordinates 
file type. It contains a title line followed by one line for 
each atom in the structure. Each line contains: the 
sequential number within the structure, an atomic 
symbol or name, X-, Y-, and Z-coordinates, the force 
field atom type number of the atom, and a list of the 
atoms connected to the current atom. Except for 
programs whose basic operation is in torsional space, all 
TINKER calculations are done from some version of 
the .xyz format.


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>Comment By: Nico (nicove)
Date: 2004-08-02 23:37

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I put two files (200 and 400 atoms). They're the only files I 
have just now. Tomorrow I should be able to send other files.

About your questions, I don't exactly know. I participate in a 
distributed computing project about protein folding 
(http://folding.stanford.edu) and I would like to see the 
proteins with jmol.

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Comment By: Miguel (michaelthoward)
Date: 2004-08-02 22:56

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I think it would be straightforward to add support for this
file format. 

It is a unfortunate that they chose .xyz as the file name
extension, since this extension was taken by SGI xmol long
ago. The good news is that this won't really hurt Jmol. 

This text description hardly qualifies as a "file format
specification". 

Q: Is there a better description available? 

Q: What is meant by "atomic symbol or name" ?

Q: What is a "force field atom type number" ?

Please send me two files ... one with only a few atoms and
one with many atoms. mi...@jm...

If you want to work on this yourself, then you should check
out the Jmol source from anonymous cvs. Look at
src/org/jmol/adapter/smarter ... ModelResolver.java &
XyzReader.java

Miguel


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