Congrats!
Egon
On Mon, Apr 13, 2015 at 11:42 PM, Robert Hanson wrote:
> Just noticed that we are at revision # 20,448.
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
On Tue, Jun 3, 2014 at 3:41 AM, Bruno P. Kinoshita
wrote:
> Let me know if you find it useful, and kudos for all the work in Jmol. It
> was my first time using it, but there was good documentation and examples,
> and the Javascript library worked very well too.
This is cool!
So, what kind of pro
Hi Jmol devs,
This JChemInf paper introduces "CH5M3D: an HTML5 program for creating
3D molecular structures":
http://www.jcheminf.com/content/5/1/46/abstract
Jmol is cited and compared to.
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht Uni
On Sat, May 11, 2013 at 9:20 PM, Angel Herráez wrote:
> Meanwhile, I have uploaded a combined J(S)mol logo-banner to the wiki,
> http://wiki.jmol.org/index.php/File:J%28S%29mol_logos13.png
> (also attached here)
In find it a bit hard to read the Jmol... as they are less bordered
than the molecule
On Sun, Jul 22, 2012 at 10:13 AM, Rzepa Henry wrote:
> I would love to sprinkle QR codes in lecture notes, and have students
> acquire the molecule on their mobile device seconds later?
QR codes basically encode a random string. Commonly, URLs, e.g. with
QRate.me for posters such as this one [0
On Wed, Nov 2, 2011 at 1:31 PM, Miguel Howard wrote:
> I suggest that you simply rename the rename the 3D math packages that
> are used by Jmol. That is, use eclipse and rename from javax.Point3i
> to org.jmol.javax.Point3i ... or something like that. We have the
> source code included in the repo
On Wed, Nov 2, 2011 at 1:28 PM, Egon Willighagen
wrote:
> On Wed, Nov 2, 2011 at 1:07 PM, Robert Hanson wrote:
>> We have two independent reports of javax.Point3i problems when Jmol Jar
>> files are compiled on a PC and run on a mac. It seems somehow the Poin3i(int
>
On Wed, Nov 2, 2011 at 1:07 PM, Robert Hanson wrote:
> We have two independent reports of javax.Point3i problems when Jmol Jar
> files are compiled on a PC and run on a mac. It seems somehow the Poin3i(int
> x, int y, int z) initializer is missing.
It sounds to me that vecmatch is missing from th
On Sun, Oct 30, 2011 at 4:04 AM, Robert Hanson wrote:
> Can that be real?
The CDK is at around 1800 a month, and Jmol has a much wider audience;
so, those numbers look comparable.
> Or is mostly robots?
That is a good question. 20% has an unknown OS, so that could very
well be robots...
Egon
On Tue, Oct 4, 2011 at 9:32 AM, Nicolas Vervelle wrote:
> I made an announcement on launchpad mailing list for the release of Jmol
> 12.2.
Did the updated for 'Dutch' came through properly?
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (h
Hi Miguel!
On Tue, Jun 7, 2011 at 6:18 PM, Miguel Howard wrote:
> Actually, I did the original marching cubes implementation.
Oops, sorry! (and cool that you are still listening in!)
> My recollection is that it did *not* calculate volume. However, it
> seems to me that it would be straightforw
Hi Bob,
I know you (right?) implemented the marching cubes algorithm to
calculate molecular surfaces... does you code also calculate the
molecular volume?
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://eg
On Fri, Jan 14, 2011 at 10:54 PM, Robert Hanson wrote:
> I see, so you need the intermediate stage, not the actual model. one problem
> was that "openClientFile" was a misnomer -- clearly the actual file by then
> is long closed.
Indeed.
> Where are you getting the AtomSetCollection from?
Well,
Bob,
the previous Jmol version allows code like this:
if (obj instanceof AtomSetCollection) {
viewer = (Viewer)jmolViewer;
viewer.openClientFile(string, string2, obj);
}
In the current stable version the openClienFile() method is no longer
present, and I do not se
2010/12/18 Angel Herráez :
> Thanks, Egon, I had already found that page of yours yesterday.
> But in practical terms I don't know what to make out of it. I haven't got CDK
> installed (and will
> not, since it exceeds my needs and understanding).
OK, point taken. Of course, you can ask on the cd
Hej Angel,
2010/12/18 Angel Herráez :
> Bob wrote:
>> A satisfying day! After my development laptop died yesterday, that is
>> especially good new.
>
> So you melted it down? ;-D
Would not surprise me either :)
>> Angel, I need you to test those V2000 files to see if they really do load
>> i
On Sun, Nov 21, 2010 at 1:01 PM, Nicolas Vervelle wrote:
> I had problems with all the files (images, molecular files, ...)
> I had to delete all the images and upload them again manually.
> Please, check if there are mistakes.
> I still have to take care of the molecular files.
I am happy you go
On Fri, Oct 22, 2010 at 12:33 PM, Rzepa, Henry wrote:
>>http://lists.apple.com/archives/Java-dev/2010/Oct/msg00248.html
>
> That expresses future aspirations, rather than testable reality. There is
> nothing for
> OS X at http://openjdk.java.net/
You can find instructions floating around on th
On Fri, Oct 22, 2010 at 12:16 PM, Rzepa, Henry wrote:
> http://www.theregister.co.uk/2010/10/21/apple_threatens_to_kill_java_on_the_mac/
>
> ""As of the release of Java for Mac OS X 10.6 Update 3, the version of Java
> that is ported by Apple, and that ships with Mac OS X, is deprecated,"
I thin
On Wed, Sep 15, 2010 at 7:38 PM, Jonathan Gutow wrote:
>
> On Sep 15, 2010, at 10:41 AM, Robert Hanson wrote:
>
>> -- proposing a NEW DEFAULT for Jmol for 12.1 and 12.0:
>> double bonds in the plane of the atoms, not twisty with
>> orientation.
> This is the default I always expected, but th
On Thu, Sep 2, 2010 at 8:55 PM, Robert Hanson wrote:
> Oh, yeah. I forgot to update them. And I don't have that laptop here. Well,
> they are all from http://stolaf.edu/depts/chemistry/mo/struc -- lots of
> examples there.
Ah, OK.
Thanx once again!
Egon
--
Dr E.L. Willighagen
Post-doc @ Uppsa
On Fri, Aug 27, 2010 at 4:44 PM, Robert Hanson wrote:
> sp3d2 and sp3d are really just combinations of sp2 or p orbitals and lobes,
> right? So it's the same thing. Just direct them where you want them -- or is
> that the problem, you haven't figured out how to direct the lobes where you
> want th
Hi Bob,
I'm writing up a short tutorial on orbital drawing, as I want to
visualize the kind of thing I represent in my ODK project [0]... Up to
sp3 everything is fine, but I was hoping you could also add sp3d and
sp3d2 hybridizations, see the nice slides at [1], and slides 21-22 in
particular. Ple
On Tue, Jul 27, 2010 at 10:39 AM, Nicolas Vervelle wrote:
> Adding @Deprecated and @Override annotations (boring, but easy)
> Starting to use Generics (that won't be simple and it will take time)
> And optimizations when I see some (for example, I have cleaned up the
> Profiling class that was usi
On Sat, Jul 24, 2010 at 8:17 PM, Nicolas Vervelle wrote:
> In fact, that would already be the case with Java 1.5.
> Generics are in Java 1.5 (Vector and so on...)
More importantly...
Replace Vector with ArrayList as much as possible, unless you access
the List by more than on thread... that will
On Sat, Jul 24, 2010 at 8:13 PM, Robert Hanson wrote:
> On Sat, Jul 24, 2010 at 1:13 PM, Robert Hanson wrote:
>> The big change would be to go to 11.6. I will leave that to my successor,
>> however, because it requires thousands of instances where Vector and
>> Hashtable and such have to be expli
On Sat, Jul 24, 2010 at 1:26 PM, Jonathan Gutow wrote:
> On Jul 24, 2010, at 6:00 AM, Nicolas Vervelle wrote:
>> On the other side, it won't be possible to compile Jmol with older
>> versions of Java.
>
> I don't think this is much of an issue as 1.4 is no longer supported.
> Jonathan
Even 1.5 is
On Sun, Jul 18, 2010 at 9:23 PM, Robert Hanson wrote:
> I'm pretty sure those are created and signed locally.
Is that supposed to happen automatically?
Egon
--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
Blog: http
origin: debian-scie...@lists.debian.org
Hi Michael,
I am not sure about that...
Bob, Nico:
are the selfSignedCertificate/* files supposed to be part of the
source distribution?
If not, should the build.xml not work without them?
On Sun, Jul 18, 2010 at 1:18 PM, Michael Banck wrote:
> I just
On Tue, Jul 13, 2010 at 9:40 PM, Miguel Howard wrote:
> Bob & Nico, we used to use a 3rd party implementation of javax.vecmath that
> followed the javax.vecmath API. That was necessary because
> javax.vecmath was not included in the standard java libraries at the
> time.
Also note that this 3rd p
Hi all,
On Wed, Jul 7, 2010 at 5:42 PM, Robert Hanson wrote:
> don't think so. Probably just make it bigger, not better.
The Java3D library has seen updates, but has the vecmath API itself
changed too? That was not clear to me from the website, and just got
back from holiday and did not have tim
On Mon, Jul 5, 2010 at 4:44 PM, Jonathan Gutow wrote:
> I was looking at the api documenttation for javax.vecmath and realized that
> the present release is 1.5.2 while we have 1.2 in Jmol. Do we want to update
> this?
There are various implementations available on the internet... not
always a
Hi Bob,
On Sat, Jun 19, 2010 at 6:04 PM, Robert Hanson wrote:
>> >> * the edit modes are quite hidden now, in the popup menu, so that
>> >> changing drawing mode takes quick a few clicks
>> >
>> > true. Suggestions?
>>
>> Toolbar?
>
> Applet?
Function keys and a 'text' in the window to show what
Hi Bob,
On Sat, Jun 19, 2010 at 5:39 PM, Robert Hanson wrote:
>> * it took me a few minutes to realize how to unset the 'delete atom' mode
>
> Suggestions? My original plan was to have icons with the selections, so that
> the top icon would change to reflect what was selected in the subdirectory.
Hi Bob,
nice work on the model kit! I have just used to draw set up the model
for a complex natural product, and that worked well...
Some observations:
* it took me a few minutes to realize how to unset the 'delete atom' mode
* it would be nice if the FF energy would be displayed somewhere
* the
On Thu, May 27, 2010 at 5:40 PM, Robert Hanson wrote:
> Of course, the caveat is that the Universal Force Field is pretty simple and
> not at all accurate in terms of real energy, but still, it's awfully fun to
> see caffeine bounce off an enzyme!
For educational purposes this is brilliant!
Bob+
On Mon, May 3, 2010 at 10:08 PM, Robert Hanson wrote:
> So with JChemPaint you can use less that sum of Jar files?
Yes.
> What is the minimum suite of necessary Jar files, I wonder.
That should be about 800kB, if I understood correctly... but the trick
is, that the applet GUI does not have the
cc:jmol-developer (following Angel)
Hi Angel, Chris,
> From: Christoph Steinbeck
> We need to be careful with statements about what "should be possible"
> until we've done it. :-)
True :)
> I'm more than happy to finance a little workshop here at the EBI or in
> Uppsala to work on a scheme to
2010/5/1 Angel Herráez :
> On 1 May 2010 at 21:20, Egon Willighagen wrote:
>
>> However, with the current design, a sub 250kB applet should be possible...
>
> That's interesting... Right now, just applet-core and applet-editor sum up
> 560 KB
I have been working on so
On Fri, Apr 30, 2010 at 7:54 PM, Robert Hanson wrote:
> Then why is it so huge ( > 4 Mb)?
I do not know why the current applet is so large. I understood that
only about 700kB is reaaly needed for drawing molecules; and a lot
more downloaded for additional but optional functionality, like InChI,
e
On Thu, Apr 29, 2010 at 6:32 AM, Robert Hanson wrote:
> Feature request #1: JME output. It's simple, concise, and I think allows for
> everything you have there.
Do you have a specification of that format?
Egon
--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of Prof. Jarl
On Thu, Apr 29, 2010 at 12:12 AM, Robert Hanson wrote:
> What I liked about JME was that it was so lightweight (30K).
Indeed. JChemPaint is not quite down to that range yet, but we are
working towards it.
Egon
--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of Prof. Jarl
cc: cdk-jchempa...@lists.sf.net
Bob, Angel,
2010/4/28 Angel Herráez :
> A few bugs or lack of features in the Javascript API of JChemPaint have
> refrained my
> progress with this. Then, JCP v3 was started with quite a reworked engine,
> and I posed great
> expectation on it, but haven't been
On Wed, Apr 28, 2010 at 7:28 PM, Robert Hanson wrote:
> 1. Add a 2D drawing tool to the Jmol applet that would provide a similar
> (though expanded) functionality of JME (and, unlike JME, would be open
> source, of course!).
Like JChemPaint?
Egon
--
Post-doc @ Uppsala University
Proteochemomet
Hi Hilmar,
On Fri, Apr 2, 2010 at 9:31 PM, Hilmar Lapp wrote:
> On Apr 2, 2010, at 2:15 AM, Egon Willighagen wrote:
>> I'll co-mentor the student from the Jmol side then.
>
> That's great, thanks Egon for helping out!
My pleasure. My previous GSoC T-shirt is getting
Hi Hilmar,
On Thu, Apr 1, 2010 at 10:22 PM, Hilmar Lapp wrote:
> What we need for this project is just a co-mentor to assist with guidance as
> far as Jmol components are concerned. I understand that Chris would be the
> primary mentor.
Yeah, Bob is Robert Hanson. He declined, and I have not hea
On Tue, Feb 9, 2010 at 9:33 AM, Rzepa, Henry wrote:
> Vendor lock in means many things.
Yes, it does.
> For example, do you worry that you are vendor locked into Acrobat from Adobe?
Which I therefore not use.
> Or Flash from Adobe.
Guilty as charged :)
> Or Silverlight from M$?
Actually, th
On Thu, Jan 28, 2010 at 9:24 AM, Rzepa, Henry wrote:
> Anyone looked at this cross compiling suite?
Hahahaha... sorry, Henry!
Had not read this one before replying to your iPad email... :(
Conclusion: I very much like to hear if someone has tried that yet?
Egon
--
Post-doc @ Uppsala Universi
On Thu, Jan 28, 2010 at 8:29 AM, Rzepa, Henry wrote:
> Who knows what niche devices such as the iPad will find, but given one target
> is reading books (and scientific journals; the number of apps for doing so
> is growing rapidly), a Jmol-less world might be beckoning. I presume the
> prosp
On Mon, Feb 1, 2010 at 10:58 PM, Robert Hanson wrote:
> But there was a price. Up until now we have had this line in build.xml:
>
> source="1.3" target="1.1"
>
> That now reads
>
> source="1.4" target="1.4"
>
> For Jmol 11.9. Is there some reason we should be sticking with th
On Tue, Jan 5, 2010 at 1:39 PM, Robert Hanson wrote:
> I mean, every time I add a character in the FIND box, Eclipse jumps to the
> next occurrance of that in the code. It's very annoying, especially when I
> make typing mistakes. Suddenly I'm in some far reaches of the code and have
> to navigate
On Tue, Jan 5, 2010 at 2:43 AM, Robert Hanson wrote:
> Suddenly (I think) Eclipse has changed its behavior on searches. I don't
> recall searches (simple CTRL-F) being incremental - going with each
> keystroke. Am I just crazy? For others using Eclipse, does it wait until you
> press a button to j
On Wed, Nov 4, 2009 at 7:57 PM, wrote:
> -version=11.8.8
> +version=11.8.8_dev
>
> +#
> -
> +
> +#version=11.8.8
> +
> # bug fix: GAMESS reader not reading BETA MOs.
> # bug fix: A function starting with "_" originally
On Mon, Nov 2, 2009 at 8:16 PM, Robert Hanson wrote:
> Egon -- that was a bug in BondCollection -- returning atomIndex, not
> modelIndex.
Ack.
> Fixed in SVN.
Ah, too bad... would have loved to make a Jmol commit again :)
> Or use
>
> int modelIndex = set.getBondAt(bondIndex).getAtom1().getMo
Bob,
I just tried the below patch, and that fixes my problem. Shall I commit?
Egon
On Fri, Oct 30, 2009 at 5:08 PM, Egon Willighagen
wrote:
> I actually have a clue:
>
> public int getBondModelIndex(int i) {
> return bonds[i].atom1.atomIndex;
> }
>
> That should re
On Fri, Oct 30, 2009 at 5:18 PM, Joe Gatewood wrote:
> This is probably more of a Java question but I know this list will offer
> useful opinions.
>
> I have the contents of a pdf file in an ArrayList. What is the most
> efficient way to load into Jmol?
That's one PDB file, right?
I think there
Bob,
On Fri, Oct 30, 2009 at 4:58 PM, Egon Willighagen
wrote:
> I have no clue why the ModelSet return 2 for the second bond... the
> input is this MDL molfile:
I actually have a clue:
public int getBondModelIndex(int i) {
return bonds[i].atom1.atomIndex;
}
That should real
Bob,
I am using 11.8.7 in Jmol and writing CML serialization... my current
code looks like (JmolMolecule actually just wraps a CMLMolecule):
List mols = new ArrayList();
ModelSet set = jmolPanel.getViewer().getModelSet();
System.out.println("model count: " + set.getModelCo
On Wed, Oct 28, 2009 at 1:49 AM, Robert Hanson wrote:
> I thought I would wait for the schema until we worked out some more details,
> but I think I'm about ready for that now. I like the Relax NG format. Is
> there anything that can take a functioning XML page and create a template
> schema from
On Tue, Oct 27, 2009 at 6:04 AM, Robert Hanson wrote:
> Who would like to help me with this so that I have a better chance of doing
> it right?
Sure. I will be away until Thu, and Fri too...
Have you made a matching XML Schema or RelaxNG already?
Egon
--
Post-doc @ Uppsala University
Homepage
On Fri, Sep 4, 2009 at 3:23 PM, Jonathan Gutow wrote:
> I may be able to make this work. It will be in a new fiscal year so
> I can probably get travel funding. I'd be willing to help with either
> workshop. Is workshop 1 appropriate for the webexport function or do
> we want an even lowe
Hi Bob,
while translating 11.8 into Dutch (updating, really), I noticed
"Executing script 1..." and "Executing script 2..." ... can you update
that make it use {0} ? Otherwise, I will early next week...
Egon
--
Post-doc @ Uppsala University
http://chem-bla-ics.blogspot.com/
---
On Thu, Aug 13, 2009 at 12:57 PM, Robert Hanson wrote:
> I think we're probably ready for 11.8. The only things I have going are
> major ideas that I don't want to get started on prior to that. How about a
> release on Tuesday?
Bioclipse 2.1 (a development series) is using RC4, and we have not
fou
On Thu, Aug 6, 2009 at 9:04 AM, Robert Hanson wrote:
> It's possible to embed the Jmol state script in the U3D file, so one can
> load the PDF file itself or the U3D file itself back into Jmol:
>
> script "filename.pdf"
>
> or
>
> script "filename.u3d"
>
> (although I did not do that with the one I
On Thu, Aug 6, 2009 at 8:38 AM, Robert Hanson wrote:
> This is a human-readable format that can be transformed into the binary U3D
> format that then can be inserted into PDB files
> using a simple command-line utility IDFConverter.exe (Windows only). The end
> result is a stunning PDF file with a
On Tue, Jun 30, 2009 at 5:59 PM, Robert Hanson wrote:
> I have gettext installed; it is running. But when it tries to do use javac
> it says:
>
> [echo] Updating messages_pt_BR.class file for JmolApplet ...
> [exec]
> C:\jmol-dev\workspace\Jmol\src\org\jmol\translation\JmolApplet>c:\j2sdk
On Wed, Jun 3, 2009 at 7:58 AM, Robert Hanson wrote:
> Well, wouldn't you know it? What started out as a simple idea turned into
> quite a challenge. But I think I'm done, and I am very interested in
> extensive testing. Sorry, Angel -- you may have to rewrite your book!
Argh... now I am going to
On Mon, Mar 30, 2009 at 4:40 PM, Jonathan Alvarsson
wrote:
> I have had some sucess. It's actually sort of working for small molecules
> now. Next step is selects in bigger proteins...
OK, then just disregard my statement. It seems to be a regular Monday
for me today... a day where nothing really
On Mon, Mar 30, 2009 at 2:24 PM, Jonathan Alvarsson
wrote:
> I am guessing org.jmol.api.JmolSelectionListener should be used for what I
> am trying to do. (Listening to selection changes in jmol). However it seems
> to not be working. I have added a JmolSelectionlistener using
> org.jmol.api.JmolV
Bob,
On Fri, Mar 27, 2009 at 4:21 PM, Robert Hanson wrote:
> The getRegistryInfo Hashtable returns information for the applet concerning
> all the available applets on ANY open browser page utilizing this JAR file.
>
> We take a very minimalist view of documentation. Sorry.
Thanx for answering a
Jonathan,
On Thu, Mar 19, 2009 at 2:37 PM, Jonathan Alvarsson
wrote:
> My fellow Bioclipse developers
I guess that would be me?
> advise me to not use trunk but rather your latest tested version.
Being the stable release, that made sense to me at the time :)
> However I am a bit confused as t
On Thu, Mar 12, 2009 at 6:13 PM, Robert Hanson wrote:
> Commands should be available via (String[])
> viewer.getProperty("object","tokenList","commands").
Thanx!
> Good luck working out all the command line possibilities. What we instead
> opted for was what is installed in the Jmol application
Hi all,
over here in Uppsala we are cooking on a Jmol application alternative,
as it allows much easier integration of third party software (such as
MM toolkits) with the Jmol viewer than the Jmol application does
itself.
Right now, we are close to a Bioclipse 2.0 release, which will feature
limi
Hi all,
not sure if this analysis was already posted here, in which case I missed it:
http://www.slideshare.net/wettel/visual-exploration-of-largescale-system-evolution-presentation-687858?type=powerpoint
It introduces a method called 'City' to visualize a code base, and
Jmol is mentioned as exa
On Sat, Oct 25, 2008 at 8:43 PM, Nicolas Vervelle <[EMAIL PROTECTED]> wrote:
> I have started configuring the Findbugs plugin for Eclipse.
> If you are interested in seeing the result, install the plugin [1] and get
> the latest version
How does it compare to PMD?
http://pmd.sourceforge.net/repor
On Mon, Oct 6, 2008 at 6:12 PM, Angel Herraez <[EMAIL PROTECTED]> wrote:
>> But browsing that list is more difficult then for finding your
>> language of choice...
>
> Why do you think that, Egon? All except one would be strange
> language names... You pick the one you understand
Well, I underst
On Mon, Oct 6, 2008 at 1:37 PM, Robert Hanson <[EMAIL PROTECTED]> wrote:
> In the interest of getting 1.6 out the door, I'd like to propose that we
> strike the en_GB translation for now and instead make that part of 1.7,
> because implementing it requires changes to GT.
>
> Then Nico or I can work
On Mon, Oct 6, 2008 at 12:08 PM, Angel Herraez <[EMAIL PROTECTED]> wrote:
>> also -- this introduces a need for translations of "English - United
>> Kingdom" in every translation. Is the plan to have these done prior
>> to 11.6? [I thought we were done with translations...]
>
> Now that this pops-u
On Mon, Oct 6, 2008 at 1:56 PM, Egon Willighagen
<[EMAIL PROTECTED]> wrote:
>> For example: a Spanish-speaking user visits a Dutch lab and will see
>> Jmol menu in Dutch.
Would you not set your browser and/or desktop to Spanish first? Jmol
would pick that up...
>> What i
On Mon, Oct 6, 2008 at 1:54 AM, Robert Hanson <[EMAIL PROTECTED]> wrote:
> also -- this introduces a need for translations of "English - United
> Kingdom" in every translation. Is the plan to have these done prior to 11.6?
> [I thought we were done with translations...]
Nothing much we can do abou
Hi Andreas,
On Thu, Aug 21, 2008 at 5:11 PM, Andreas Prlic <[EMAIL PROTECTED]> wrote:
> the graphical image for the BioJava data model in that blog is not
> completely correct. It is true that it follows the
> Interface/Implementation approach,but the data model is more
> hierarchical than shown
Hi all,
the PDBReader of Jmol is of high quality, and certainly much better
than the CDK one. There is also the BioJava PDBReader, and the
question was popped if the CDK should adopt the BioJava or Jmol
reader, both better, though I am not familiar with the BioJava one...
now, that would involve c
On Thu, Aug 14, 2008 at 4:54 PM, Miguel <[EMAIL PROTECTED]> wrote:
> Be advised that there are other (splinter) groups working on Java
> implementations. For example, there is a GNU compiler for Java and there
> was (is?) a GNU effort to reimplement all of the Java class libraries.
That would be C
On Sun, Jun 8, 2008 at 7:53 AM, Tim Miller <[EMAIL PROTECTED]> wrote:
> I am writing to inquire if there are any plans to support the
> icedtea/GCJ java plugin. Currently, when I try to run the Jmol applet,
> with this plugin in 64 Ubuntu 8.04, I get:
>
> PIPE: appletviewer read: instance-6449-2
>
Hi Alexandre,
looks interesting indeed. Have to determine the exact scope yet, as
LIMS is a rather broad term... myself, I have been working in the last
9 months on MetWare, for managing metabolomics (GC/MS, LC/MS) data and
derived results... [0] But we did not want to go the full LIMS path,
so it
On Fri, Mar 28, 2008 at 9:30 PM, Bob Hanson <[EMAIL PROTECTED]> wrote:
> It's a separate thread, so you can do odd things, like rotate the model
> while it is minimizing. --- or even set it spinning, I think! I'm
> thinking what we need is some sort of a minimization callback so that
> the user
On Fri, Mar 28, 2008 at 8:07 PM, Bob Hanson <[EMAIL PROTECTED]> wrote:
> I had some very strange cross-SVN branch thing going on there. A few
> files in my checked out Trunk turned out to be in my branch, so I was
> committing changes to a branch and a trunk at the same time. I didn't
> know th
All,
On Sun, Mar 23, 2008 at 3:03 PM, Bob Hanson <[EMAIL PROTECTED]> wrote:
> Egon, I'm worried I detect sarcasm in that message. Just asking for
> clarification.
No sarcasm intended in that message!
> Egon Willighagen wrote:
> >> There's no need to worry
cc: cdk-devel
On Sun, Mar 23, 2008 at 2:08 PM, Geoffrey Hutchison
<[EMAIL PROTECTED]> wrote:
> On Mar 23, 2008, at 2:16 AM, Egon Willighagen wrote:
> > Unless this would happen... though this would require everyone who
> > every contributed to the code to agree wit
On Sun, Mar 23, 2008 at 7:10 AM, Bob Hanson <[EMAIL PROTECTED]> wrote:
> * I've included the license blocks from the C++ code -- currently
> stating GPL, not LGPL.
That is the correct thing to do.
> I don't really know how that works when you do a substantial rewrite and
> code language translati
Hi all,
the .po files have now been approved:
https://translations.launchpad.net/jmol/11.4/+pots/jmol
Please feel free to play with the system, and report your experience.
Egon
--
http://chem-bla-ics.blogspot.com/
-
On Sat, Mar 15, 2008 at 5:10 PM, Nicolas Vervelle
<[EMAIL PROTECTED]> wrote:
> A few questions / remarks.
>
> Are the files automatically updated from svn on the launchpad.net website,
> or does it need a manual intervention to update them ?
> Also, how is the commit done ? Manual intervention o
On Sat, Mar 15, 2008 at 3:40 PM, Egon Willighagen
<[EMAIL PROTECTED]> wrote:
> Now, LP also has a nice web based tool for translating .pot files...
> I'm interested in playing with that for Jmol, and will set up things.
> Hopefully, it will increase the number of transla
Hi all,
Launchpad.net (LP) is something developed by Canonical, which is the
company behind the Ubuntu GNU/Linux distribution.
Now, LP also has a nice web based tool for translating .pot files...
I'm interested in playing with that for Jmol, and will set up things.
Hopefully, it will increase the
On Fri, Mar 7, 2008 at 6:32 PM, Bob Hanson <[EMAIL PROTECTED]> wrote:
> Wow - very nice, Angel!
Indeed, very nice!
> Additional capabilities you may want to mention:
Some minor points:
You could also point out this 'poster' Miguel Howard and I had at some
electronic conference:
http://precedi
Hi all,
I just had trouble committing to SVN, and it likely has to do with
this message from SF:
"( 2008-03-06 14:23:47 - SourceForge.net Web Site ) In support of
improved security, all SourceForge.net user passwords have been
expired and must be changed upon next login. CVS, Subversion and S
On Tue, Mar 4, 2008 at 8:32 PM, Bob Hanson <[EMAIL PROTECTED]> wrote:
> >I'd like to let you know that next week I will be participating --as
> >a Jmol representative ;-) --
I am really happy that you found time to do it.
Have fun!
Egon
--
http://chem-bla-ics.blogspot.com/
On Sun, Mar 2, 2008 at 12:09 PM, Nicolas Vervelle
<[EMAIL PROTECTED]> wrote:
> Apart from simply being up to date, I think the main advantage is that the
> new LGPL is compatible with more other licenses (Apache license for
> example). http://www.gnu.org/licenses/quick-guide-gplv3.html
> That will
On Sat, Mar 1, 2008 at 7:14 PM, Nicolas Vervelle
<[EMAIL PROTECTED]> wrote:
> Should we move to the new version of the GNU LGPL (v3) instead of the
> current one (v2.1) ?
What advantages do you see?
Egon
--
http://chem-bla-ics.blogspot.com/
--
On Jan 22, 2008 1:53 PM, Rajarshi Guha <[EMAIL PROTECTED]> wrote:
> On Jan 22, 2008, at 2:32 AM, Egon Willighagen wrote:
> > Rajarshi, has your resource a REST-like interface that supports
> > InChIKey? Something like
> >
> > http://www.chembiogrid.org/ch
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