Is it real to take Jmol as a basis for editor? Add, delete, create atoms.
Construct multiatomic structures, manipulate them. Fill some space with same
atoms... I'm interested mainly in crystallography. May be someone can manage or
help in this way. What is needed, time for realising it?
Egon,
>Ah, interesting! Are these plan for creating an Open Source product?
>Bioclipse could actually be a perfect basis for such functionality.
As I understand, Bioclipse using Jmol only as a viewer. I'd like to extend 3d
editor.. I'm thinking about OpenSource, of course. But to begin new project or
continue same - don't know.
Bob,
>1) Which version of Jmol are you using?
I used Version 11.6.20.
>2) If you can, use a Jmol.jar file that was build with <property name="debug"
>value="on" /> in build.xml
Can you give me the link to it, please. I've downloaded some, but they have
"off" property value.
> But I think your main problem is that you aren't fully allocating the
> viewer:
I've fixed it with
viewer.evalString("ZAP");
But another NullPointerException still appears in exceptions, in line with:
viewer.openClientFile("", "", methane);
Where methane created like in example.
If newer version solves this problem, I'll try it.
-----Original Message-----
From: Robert Hanson <[email protected]>
To: Jmol Developers <[email protected]>, [email protected]
Date: Mon, 6 Apr 2009 11:48:17 -0500
Subject: Re: [Jmol-users] Jmol + cdk
> Aidar,
>
> [switching to Jmol Developers list]
>
>
> I'm really glad you are working with this. No one has updated this for some
> time, and I'm not surprised it may be causing some difficulty for you.
>
> 1) Which version of Jmol are you using?
> 2) If you can, use a Jmol.jar file that was build with
>
> <property name="debug" value="on" />
>
> in build.xml
>
> But I think your main problem is that you aren't fully allocating the
> viewer:
>
>
> /**
> * This is the main access point for creating an application
> * or applet viewer. After allocation it is MANDATORY that one of
> * the next commands is either
> *
> * viewer.evalString("ZAP");
> *
> * or at least:
> *
> * viewer.setAppletContext("",null,null,"")
> *
> * One or the other of these is necessary to establish the
> * first modelset, which might be required by one or more
> * later evaluated commands or file loadings.
> *
> *
> * @param awtComponent
> * @param jmolAdapter
> * @return a JmolViewer object
> */
> static public JmolViewer allocateViewer(Component awtComponent,
> JmolAdapter jmolAdapter) {
>
>
>
>
> That's what is causing that null pointer problem. Because this is a common
> problem, Jmol 11.7 has a better interface:
>
> /**
> * This is the main access point for creating an application
> * or applet viewer. In Jmol 11.6 it was manditory that one of
> * the next commands is either
> *
> * viewer.evalString("ZAP");
> *
> * or at least:
> *
> * viewer.setAppletContext("",null,null,"")
> *
> * One or the other of these was necessary to establish the
> * first modelset, which might be required by one or more
> * later evaluated commands or file loadings.
> *
> * Starting with Jmol 11.7, setAppletContext is rolled into
> * allocateViewer so that the full initialization is done
> * all at once.
> *
> *
> * @param awtComponent
> * @param jmolAdapter
> * @param htmlName
> * @param documentBase
> * @param codeBase
> * @param commandOptions
> * @param statusListener
> * @return a JmolViewer object
> */
> static public JmolViewer allocateViewer(Component awtComponent,
> JmolAdapter jmolAdapter,
> String htmlName, URL documentBase,
>
> URL codeBase,
> String commandOptions,
> JmolStatusListener statusListener)
> {
>
>
> and
>
> /**
> * OK, but safer to assign htmlName, URL bases, comandOptions, and
> statusListener now.
> *
> * @deprecated
> * @param awtComponent
> * @param jmolAdapter
> * @return a viewer
> */
> public static JmolViewer allocateViewer(Component awtComponent,
> JmolAdapter jmolAdapter) {
> return Viewer.allocateViewer(awtComponent, jmolAdapter, null, null,
> null, null, null);
> }
>
>
>
> Bob
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