-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On Thursday 19 February 2004 13:06, Tommi Hassinen wrote:
> On Thu, 19 Feb 2004, E.L. Willighagen wrote:
> > PS, it would also be nice if the plugin could also work on a local
> > Ghemical copy...
>
> Yes, I think it should work both with local and rem
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On Thursday 19 February 2004 11:17, Tommi Hassinen wrote:
> I have got an idea about a plugin that I would like to write for Jmol. I
> have checked out the sources, and duplicated the "DirBrowser" plugin class
> for my own purposes. When I studied the
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On Thursday 19 February 2004 12:46, Tommi Hassinen wrote:
> On Thu, 19 Feb 2004, Miguel Howard wrote:
> > Tommi wrote:
> > > Perhaps I could describe my plugin plan a bit. The plugin would make
> > > some comp.chem. methods available into Jmol. It woul
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On Thursday 19 February 2004 13:22, Miguel Howard wrote:
> The design philosophy behind the JmolModelAdapter interface is that it is
> the *proper* and *only* way to feed molecular models into Jmol. I think
> that it is very important that we maintain
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On Thursday 19 February 2004 12:22, Tommi Hassinen wrote:
> On Thu, 19 Feb 2004, E.L. Willighagen wrote:
> Thanks, I'll try it later in the evening.
Ok, thanx. This is something that's important to the plugin interface. I'll
explore it this week. Oth
On Friday 20 February 2004 14:15, Tommi Hassinen wrote:
> > @@ -102,6 +102,6 @@ public class JmolEditBus implements CDKE
> > }
> >
> > public ChemFile getChemFile() {
> > - -throw new NoSuchMethodError();
> > +return (ChemFile)viewer.getClientFile();
> > }
> > }
>
>
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On Thursday 19 February 2004 12:31, Miguel Howard wrote:
> Tommi wrote:
> > Perhaps I could describe my plugin plan a bit. The plugin would make
> > some comp.chem. methods available into Jmol. It would read the current
> > atoms/bonds from Jmol,
>
> T
Egon wrote:
>> On Thu, 19 Feb 2004, Miguel Howard wrote:
>> > Can you tell me a little about the ghemical?
>
> Will you be using the Ghemical Reader in CDK?
Probably. If Tommi sends the data back in Ghemical format.
> BTW, the link is: http://bioinformatics.org/ghemical/
Good.
[snip]
> If you
On Thu, 19 Feb 2004, E.L. Willighagen wrote:
> Could you try this:
>
> - --- src/org/openscience/jmol/app/JmolEditBus.java 17 Feb 2004
15:36:02
> +++ src/org/openscience/jmol/app/JmolEditBus.java 19 Feb 2004
11:03:48
> @@ -102,6 +102,6 @@ public class JmolEditBus implements CDKE
>
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On Friday 20 February 2004 12:18, Tommi Hassinen wrote:
> On Thu, 19 Feb 2004, Miguel Howard wrote:
> > Can you tell me a little about the ghemical?
Will you be using the Ghemical Reader in CDK?
BTW, the link is: http://bioinformatics.org/ghemical/
On Thu, 19 Feb 2004, Miguel Howard wrote:
> Tommi,
>
> Can you tell me a little about the ghemical?
It's a molecular modelling program written in C++. Currently it is split
in 2 parts:
libghemical : only contains the core functionality (no graphics
or file I/O), has a built-in molecular
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On Thursday 19 February 2004 11:38, Tommi Hassinen wrote:
> On Thu, 19 Feb 2004, E.L. Willighagen wrote:
> > > Could you please tell me about the status of the JmolEditBus class?
> >
> > Which Jmol version are you refering too? Jmol HEAD, or Jmol from
Egon,
[snip - Miguel's ranting about JmolModelAdapter]
I truly apologize ... I should have looked at the JmolEditBus code before
I started lecturing about good design.
The method that you are using ... JmolViewer.openClientFile() ... is just
fine. The way that you implemented it is good.
Becaus
Tommi,
Can you tell me a little about the ghemical?
What is the input format?
> I'll learn about cgi and web servers before I start anything at the
> server side.
Good.
> I can start from client side by first figuring out how to
> get and set atoms and bonds from/to Jmol classes.
Be advised t
On Thu, 19 Feb 2004, Miguel Howard wrote:
> Let me know if you need more reasons :-)
>
> Clearly this is your project and you should do what you want. But my
> strong recommendation is that you seriously evaluate the web-server
> approach.
Ok, thanks for your advice. :)
I'll learn about cgi and
Tommi,
> On Thu, 19 Feb 2004, Miguel Howard wrote:
>
>> If Ghemical does not have a server then I recommend that you access it
>> through a .cgi on a web server.
>
> There is no such server yet. However, the latest version in CVS works as
> a bonobo component (bonobo is the gnome component system)
On Thu, 19 Feb 2004, Miguel Howard wrote:
> If Ghemical does not have a server then I recommend that you access it
> through a .cgi on a web server.
There is no such server yet. However, the latest version in CVS works as a
bonobo component (bonobo is the gnome component system). There is a simpl
>> 500:remote.server.net
>>
>> where "500" is the port number and "remote.server.net" is the IP
>> address of the remote server. In this case there should be a server
>> process listening the port 500 in the remote system, which would
>> receive the requests from plugins and provide the servi
>> Passing the structure back to Jmol means that you need to implement
>> the JmolModelAdapter interface. That is the API for feeding structures
>> to Jmol.
>
> Miguel, the plugins use the CDKEditBus interface for this... Jmol's
> jmol/app/JmolViewer.java provides this interface to plugins...
>
>>
On Thu, 19 Feb 2004, E.L. Willighagen wrote:
> Yes, I think so... but let's see what Miguel has to say about it...
Ok, I'm not in a hurry with this... :)
> PS, it would also be nice if the plugin could also work on a local Ghemical
> copy...
Yes, I think it should work both with local and remo
On Thu, 19 Feb 2004, Miguel Howard wrote:
> Tommi wrote:
> > Perhaps I could describe my plugin plan a bit. The plugin would make
> > some comp.chem. methods available into Jmol. It would read the current
> > atoms/bonds from Jmol,
>
> This sounds like good functionality.
> I think that Jmol shoul
Tommi wrote:
> Perhaps I could describe my plugin plan a bit. The plugin would make
> some comp.chem. methods available into Jmol. It would read the current
> atoms/bonds from Jmol,
This sounds like good functionality.
I think that Jmol should provide iterators for this purpose.
> send them to a
Egon wrote:
>> Could you please tell me about the status of the JmolEditBus class?
>
> Which Jmol version are you refering too? Jmol HEAD, or Jmol from the b6
> branch? (If you just did cvs co Jmol, then it would be the default =
> HEAD...)
>
> I'll have alook at the source code how difficult this
On Thu, 19 Feb 2004, E.L. Willighagen wrote:
> Could you try this:
>
> - --- src/org/openscience/jmol/app/JmolEditBus.java 17 Feb 2004 15:36:02
> +++ src/org/openscience/jmol/app/JmolEditBus.java 19 Feb 2004 11:03:48
> @@ -102,6 +102,6 @@ public class JmolEditBus implements CDKE
>
On Thu, 19 Feb 2004, E.L. Willighagen wrote:
> > Could you please tell me about the status of the JmolEditBus class?
>
> Which Jmol version are you refering too? Jmol HEAD, or Jmol from the b6
> branch? (If you just did cvs co Jmol, then it would be the default = HEAD...)
This is the cvs HEAD ver
Hello.
I have got an idea about a plugin that I would like to write for Jmol. I
have checked out the sources, and duplicated the "DirBrowser" plugin class
for my own purposes. When I studied the JmolEditBus class, I saw that the
methods getChemModel() and getChemFile() are not yet implemented.
Co
26 matches
Mail list logo
