For those Pythonistas out there, translating Rolf's command line command to one
to be executed in the Jmol download folder using `1crn` that comes in the
`data` folder would be:
cat ./jsmol/data/1crn.pdb | python -c "import sys; print 'load DATA
\"mydata\"\n';[sys.stdout.write(line) for line in sys.stdin]; print 'END
\"mydata\"\n'" | java -jar Jmol.jar -s -
I posted a gist of it at
https://gist.github.com/fomightez/7692b540ff3c5d817bf5.
It uses Python 2; most computers still have Python 2 installed by default.
Wayne
------------------------------
Message: 12
Date: Fri, 2 Oct 2015 17:12:25 +0200
From: Rolf Huehne <rhue...@fli-leibniz.de>
Subject: Re: [Jmol-users] Jmol reads a structure file from a pipe or
system input
To: jmol-users@lists.sourceforge.net
Message-ID: <560e9ed9.4000...@fli-leibniz.de>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 10/02/2015 04:51 PM, Robert Hanson wrote:
> Ah, OK. That's it. Thanks, Rolf.
>
>
> Dwey, try wrapping your structure data with
>
> load DATA "mydata"
> ...
> end "mydata"
>
> and then use the Jmol -s - option.
>
> -s indicates to read a script file, and "-" indicates that we are using
> System.in for that file data.
>
>>From jmol -h:
>
> -s,--script <arg> script file to execute or '-' for
> System.in
>
> That is sure to work.
>
>
> My perl is quite rusty, but it may be as simple as:
>
> cat pdb1deh.ent | perl -ne 'BEGIN { print "load DATA \"mydata\"\n";} END {
> print "END \"mydata\"\n";}' | java -jar Jmol.jar -s -
>
Between the 'BEGIN {}' and 'END {}' section there is missing what to do
for each line of the file ('print $_;') but if it is added it works for me:
cat /scratch/pdb/pdb/pdb1deh.ent | perl -ne 'BEGIN { print "load DATA
\"mydata\"\n";} print $_; END { print "END \"mydata\"\n"; }' | java
-jar Jmol.jar -s -
Regards,
Rolf
--
Rolf Huehne
Postdoc
Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany
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