Good morning to you, Robert,
Thanks a lot for your welcome and your notes!
I answer you:
*R_1*: for now, the python script works in local on a sdf file as test,
manually downloaded from PubChem, but after solved this item to generate
the idtf file in a webserver, the next step will be implement the python
script with the possibility to fetch a molecule/macromolecule from the web
(Protein Data Bank, PubChem, and so on), downloading it in a folder on my
remote webserver (for example with a wget command or something like that)
to perform then (server side) the Jmol script on it, without user
interface, only to generate the idtf file, to finally obtain a 3D pdf
visualized in the web browser, that you can download. As first idea, I
tried to use a PyMOL script (which is in python too) to export the idtf
file, but perhaps there is something wrong in its exporting, becouse the
idtf file is much smaller than the Jmol idtf file, and PyMOL seems to
export only if the style is setted to cartoon (so, only for
macromolecules), but it fails to export the idtf for small molecule
visualized as sticks, for example (for this I need to ask to PyMOL
mailing-list; probably, the PyMOL's idtf exporter must be implemented for
this... I don't know).
For this reason, I'm using Jmol with the option to launch commands from a
script in silent mode, but there is the problem for java. I asked for java
to my server hosting, but I thought to upload a portable version of java
just to launch Jmol for that script (in a linux shell this works, and the
webserver is based on a linux platform; so, integrating all in a python
script should be working... I'm testing it).
*Q*: Among other things, I was looking for a way to insert a command to
hide the non-polar hydrogens into the Jmol script, but I have not found the
way; I would also ask for this ... The PyMOL command, for a molecule like
the pp2 (= CID_4878), would be:
*cmd.hide("(CID_4878 and hydro and (elem c extend 1))")*
Just now, making a google search, I found
this<http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?_USE=HTML5>page,
where is a "PyMOL session - dna" example:
*Q*: Probably, is possible to integrate pymol with jmol scripting to hide
non-polar hydrogens:
*javascript:Jmol.script(jmolApplet0,'load data/dna.pse')*
where dna.pse is a PyMOL session file, but probably could be a pymol script
(.pml) too.
Thanks for your advice! I tried to test JmolData.jar instead of Jmol.jar,
using that portable java:
==================================
*riccardo@RickLaptop:/var/www/db/jmol$ ../java/jre1.6.0_21/bin/java -jar
./JmolData.jar --helpSome exception occurred!:
java.lang.NullPointerExceptionorg.jmol.i18n.Resource - -1 -
getResourceorg.jmol.i18n.GT <http://org.jmol.i18n.GT> - -1 -
addBundleorg.jmol.i18n.GT <http://org.jmol.i18n.GT> - -1 -
addBundlesorg.jmol.i18n.GT <http://org.jmol.i18n.GT> - -1 -
<init>org.jmol.i18n.GT <http://org.jmol.i18n.GT> - -1 -
getTextWrapperorg.jmol.i18n.GT <http://org.jmol.i18n.GT> - -1 -
_org.openscience.jmol.app.JmolApp - -1 -
getOptionsorg.openscience.jmol.app.JmolApp - -1 -
parseCommandLineorg.openscience.jmol.app.JmolData - -1 - mainSome exception
occurred!: java.lang.NullPointerExceptionorg.jmol.i18n.Resource - -1 -
getResourceorg.jmol.i18n.GT <http://org.jmol.i18n.GT> - -1 -
addBundleorg.jmol.i18n.GT <http://org.jmol.i18n.GT> - -1 -
addBundlesorg.jmol.i18n.GT <http://org.jmol.i18n.GT> - -1 -
<init>org.jmol.i18n.GT <http://org.jmol.i18n.GT> - -1 -
getTextWrapperorg.jmol.i18n.GT <http://org.jmol.i18n.GT> - -1 -
_org.openscience.jmol.app.JmolApp - -1 -
getOptionsorg.openscience.jmol.app.JmolApp - -1 -
parseCommandLineorg.openscience.jmol.app.JmolData - -1 - mainusage:
Jmol -o,--noconsole no console -- all output to
sysout -c,--check check script syntax only - no file
loading -k,--kiosk kiosk mode -- no
frame -C,--checkload check script syntax only - with file
loading -s,--script script file to execute or '-' for
System.in -q,--quality JPG image quality (1-100; default
75) or PNG image compression (0-9; default 2,
maximum compression 9) -g,--geometry window width x height,
e.g. -g500x500 -p,--printOnly send only output from print
messages to console (implies
-i) -x,--exit exit after script (implicit with
-n) -j,--jmolscript2 Jmol script to execute AFTER -s
option -J,--jmolscript1 Jmol script to execute BEFORE -s
option -P,--port port for
JSON/MolecularPlayground-style
communication -D <property=value> supported options are given
below -I,--input allow piping of input from
System.Input -L,--nosplash start with no splash
screen -M,--multitouch use multitouch interface
(requires "sparshui"
parameter -R,--restricted restrict local file
access -T,--headlessmaxtime headless max time
(sec) -b,--backgroundtransparent transparent
background -d,--debug debug -h,--help
give this help page -i,--silent silent startup
operation -l,--list list commands during script
execution -m,--menu menu file to
use -n,--nodisplay no display (and also exit when
done) -r,--restrictSpt restrict local file access (allow
reading of SPT
files) -t,--threaded independent command
thread -w,--write CLIP or
GIF|JPG|JPG64|PNG|PPM:filenameFor example:Jmol -ions myscript.spt -w
JPEG:myfile.jpg > output.txtThe -D options are as follows (defaults in
parenthesis) and must be called preceding '-jar Jmol.jar':
cdk.debugging=[true|false] (false) cdk.debug.stdout=[true|false] (false)
display.speed=[fps|ms] (ms) logger.debug=[true|false] (false)
logger.error=[true|false] (true) logger.fatal=[true|false] (true)
logger.info <http://logger.info>=[true|false] (true)
logger.logLevel=[true|false] (false) logger.warn=[true|false] (true)
plugin.dir (unset)
user.language=[ca|cs|de|en_GB|en_US|es|fr|hu|it|ko|nl|pt_BR|tr|zh_TW]
(en_US)riccardo@RickLaptop:/var/www/db/jmol$*
==================================
*Q*: Is it working, or is there something wrong? It seems that I can simply
replace the previous command in this way:
*<absolute path>/java -jar ./JmolData.jar -o -s <absolute path>/jmol.spt -n*
*R_2*: For this particular script, a Jmol applet (Java or HTML5) is not
required, for what I said above (I need only to export the idtf file, in
silent mode, without 3D GUI), because I simply want a form in which the
user can insert some preferences (like CID molecule, style, etc) to export
only the pdf.
Good to know about the html5 version of Jmol: it works on mobile devices
too!...
Only now I see that you are the same author of
this<http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?_USE=HTML5>web
page: I sent you an email just now :-)
It seems that the HTML5 version of Jmol is missing of the idtf exporter...
so I necessary need of the java version.
I will try JmolData.jar in the command to see what happens on local
webserver.
Thanks a lot,
Riccardo
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