This is done. See http://chemapps.stolaf.edu/jmol/Jmol-13.zip
___JmolDate="$Date: 2013-04-03 12:40:49 -0500 (Wed, 03 Apr 2013) $"
___JmolVersion="13.1.15_dev_2013.04.03"
new feature: Jmol/JmolData application -I flag accepts input from System.in
and command piping:
type t.spt | jmol -I start Jmol with this
script
Note: if you use a pipe, be sure to make "exitJmol" the
last command of the script
Add -o for output to System.out. Without the pipe, we are
going to control Jmol
from a Jmol> prompt on the
command line console
jmol -Io see messages on input console
...messages from Jmol
Jmol> background red;load 1crn.pdb;....
...messages from Jmol
Jmol> exitJmol
Add -n for headless operation (will not exit automatically).
type t.spt | jmol -Ion
Note: if you use a pipe, be sure to make "exitJmol" the
last command of the script
Add -i for silent operation (no writing to System.output).
bug fix: {;...;} syntax does not work in 13.1
On Fri, Mar 22, 2013 at 3:30 AM, Paolo Tosco <[email protected]> wrote:
> Dear all,
>
> is there a way to pipe commands into Jmol?
> For instance, PyMOL has a "-p" command line option which allows this. I
> use this feature in Open3DQSAR/Open3DALIGN to visualize molecules and
> update the PyMOL viewport while the program is running: thus, PyMOL acts
> as the graphical front-end of my command line tool, somehow, and the
> program keeps piping commands until it quits.
> Jmol has the "-s -" option, but commands entered on stdin are not
> executed until EOF is met (i.e., until you press CTRL+D).
>
> Is there a way to make Jmol execute commands after each newline, while
> keeping listening on stdin, and quitting when EOF is met, as does PyMOL
> with the "-p" option? I would very much like to implement Jmol as an
> alternative front-end for Open3DQSAR/Open3DALIGN, and this feature would
> enable me to do that very smoothly.
>
> Thanks, best regards
> Paolo
>
> --
> ==========================================================
> Paolo Tosco, Ph.D.
> Department of Drug Science and Technology
> Via Pietro Giuria, 9 - 10125 Torino (Italy)
> Tel: +39 011 670 7680 | Mob: +39 348 5537206
> Fax: +39 011 670 7687 | E-mail: [email protected]
> http://open3dqsar.org | http://open3dalign.org
> ==========================================================
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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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