I've created a simple Swing GUI and embedded two JmolPanel instances, each
constructed as recommended in
Integration.javahttp://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/examples/basic/org/jmol/Integration.java?revision=17001view=markup.
Upon launching the application from Eclipse IDE, I
Is it possible to reduce the minimum size of an AppConsoleinstance?
I have it embedded in a JTabbedPane and it's enforcing a larger minimum
size of that component than I'd like.
Many thanks for your time.
David
--
It seems that the prepended path is the directory Jmol's running in.
I've tried compiling my JAR and running outside of Eclipse; the same thing
happens.
I'd be grateful for help with this, since I can find no mention of #NOC# in
the documentation and can do nothing without loading a file.
Many
I'm seeking v13.x API documentation online but haven't found mention of it
under the homepage http://jmol.sourceforge.net/.
Is the link there somewhere and I've missed it?
David
--
Everyone hates slow websites. So do we.
Thanks. It seems to be working now for me.
Great! And the solution was...?
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
Hi David
I'm afraid I have no experience in building apps, but as a first line of attack
I'd
ask: is this problem restricted to the use of 2 JmolPanels?
To me it seems indeed that the path is not being properly parsed and you get
a mixture of the base path + the chosen path.
Another thng to
There's probably no updated API documentation written anywere
Bob may tell you for sure what's the state, or towhat extent you can keep
using the old one.
--
Everyone hates slow websites. So do we.
Make your web apps
Thank you for your suggestions Angel.
I've tried removing all references to one of the JmolPanel instances and
including only one instead. The same problem occurs, unfortunately.
Loading a file using the console script load FILES path/to/my.cif worked
as expected; no error was seen.
So the
Ok thanks Angel.
I'll leave this query here - I just checkout out the source and can see
there's no Javadoc'ing used, which was what I sought.
David
On 2 February 2013 13:01, Angel Herráez angel.herr...@uah.es wrote:
**
There's probably no updated API documentation written anywere
Bob may
Amendment: no Javadoc'ing *in the API sections where I was seeking it* (the
popup classes).
David
On 2 February 2013 15:09, N David Brown hubd...@gmail.com wrote:
Ok thanks Angel.
I'll leave this query here - I just checkout out the source and can see
there's no Javadoc'ing used, which was
This problem is caused by the jcd.setSize call in AppConsole.
I recommend modifying jcd to public visibility. It's not possible to extend
AppConsole in the same package, since this fails compilation with signing
errors due to the same package name in the main project and the Jmol
dependency.
..actually the correct field to change is
JmolConsole#externalContainerwhich has
protected visibility.
On 2 February 2013 16:19, N David Brown hubd...@gmail.com wrote:
This problem is caused by the jcd.setSize call in AppConsole.
I recommend modifying jcd to public visibility. It's not
I'll help you, but I'm traveling today and tomorrow. #NOC# is a marker
that we add to indicate that no cartoons are to be automatically added:
void openFile() {
String fileName = (new
Dialog()).getOpenFileNameFromDialog(viewerOptions,
viewer, null, historyFile,
Thanks Bob. It's not urgent so please just come back to me when you can.
As a workaround I subclassed AppConsole , allowing me to shrink its minimum
size and run scripts programmatically,
Then I created my own buttons in the application GUI to select files then
execute a load filepath command on
Isn't AppConsole() already public? jcd is public as well. I think you are
using the 13.0 branch rather than the trunk. As a code developer, you need
to use the trunk.
On Sat, Feb 2, 2013 at 6:19 PM, N David Brown hubd...@gmail.com wrote:
This problem is caused by the jcd.setSize call in
If you extend the class, then protected will work for you.
On Sat, Feb 2, 2013 at 7:05 PM, Robert Hanson hans...@stolaf.edu wrote:
Isn't AppConsole() already public? jcd is public as well. I think you are
using the 13.0 branch rather than the trunk. As a code developer, you need
to use the
I'm being an idiot - yes, of course you're right.
I first saw the call to jcd.setSize(...) in AppConsole source and noted it
had default visibility which causes the problem I stated.
My brain then didn't register the protected on externalContainer which
jcdgets assigned to, despite me noting
The documentation notes that SMILES layouts are generated remotely via HTTP.
Is the service providing the force-generated layout storing any information
about these structures?
I wouldn't want sensitive data to be accessed by others.
Many thanks,
David
My campus have moved its email services so I may have missed something
yesterday.
Oracle has released (yesterday) an update for Java, patching fifty (yes 50!!)
critical vulnerabilities. Today, Apple released an update for Java on Snow
Leopard.
J. Philip Bays
Emeritus Professor of
Thank you Angel and Pino for your reports.
Curiously, after seeing the sluggishness that I reported consistently
for many days, now I cannot repeat it. With the same Java 1.7.0_11 on
Windows 7, now I am getting instantaneous responses in FirstGlance in
Jmol, and zoomto is now smooth. I am
What is a layout? Jmol uses the CACTUS server at NIH/NCI to translate
SMILES strings to 3D.
On Sat, Feb 2, 2013 at 7:44 PM, N David Brown hubd...@gmail.com wrote:
The documentation notes that SMILES layouts are generated remotely via
HTTP.
Is the service providing the force-generated layout
A force-directed
layouthttp://en.wikipedia.org/wiki/Force-directed_graph_drawing .
It's useful if you don't need the accuracy of molecular dynamics, and
instead just want a semi-realistic layout for interaction with a 3D
molecule.
I'm not familiar with CACTUS. A quick google suggests the service
David,
On InChI, SMILES, and most common IUPAC, the Resolver structure is calculated
by CATVS. Name is look-up.
http://www2.ccc.uni-erlangen.de/software/cactvs/whatis.html
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Feb 2, 2013, at 4:07 PM, N David Brown wrote:
A
Nice concise summary in that link, Otis. Thank you for elucidating.
David
On 2 February 2013 21:34, Otis Rothenberger osrot...@chemagic.com wrote:
David,
On InChI, SMILES, and most common IUPAC, the Resolver structure is
calculated by CATVS. Name is look-up.
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