On Sun, Jun 30, 2013 at 10:17 PM, James <[email protected]> wrote:
> Hi,
>
> Are .hin comments (designated by a line starting with a semicolon)
> available as a variable in jmol, or should I just parse them directly
> (e.g., from getProperty fileContents)?
>
>
You should parse them. If you are having any problem with HIN files let me
know. Haven't done anything with that reader in a long long time.
> And, the Jmol wiki says:
>
> "*at#* is the number identifying the atom in the molecule (must start
> with 1 and be continuous through a molecule). Therefore a combination of
> atom number and molecule number uniquely identifies an atom in a file. "
>
> Does that mean that, unlike I believe can occur with a pdb, .hin atom
> numbers are never arbitrarily changed? Or, does it just mean "At any given
> time, there is a unique combination, but that combination is not guaranteed
> to be the same from time to time (e.g., if you add or delete atoms)"?
>
There is something called "atomIndex" that goes from 0 to the end of all
files read. Each atom has a distinct number in this.
There is something else called "atomNo" that is pulled in from the file.
This could have duplicates in a file or across multiple files.
Deleting atoms does not change either of these numbers.
>
> Thanks,
> James
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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