jmol-developers — Detailed discussions about the source code by and for Jmol developers

Re: [Jmol-developers] cml in jmol applet

[Bradley A. S. <br...@ba...>]

Encoding is an issue for the XML parser. Jmol code has little to do with
this; however, please send me a copy of the file which doesn't work, and I
will attempt to diagnose the problem.

Thanks,
  Bradley

----- Original Message -----
From: "Long JW (John)" <lo...@uc...>
To: <jmo...@li...>
Sent: Monday, May 21, 2001 8:44 AM
Subject: RE: [Jmol-developers] cml in jmol applet


> In Charlie's example code:
>
> > <?xml version="1.0" encoding="UTF-8"?>
> >
> There is also an issue with the encoding.
> In our testing, adding the first two lines you mention is not enough. If
the
> encoding is present, it cannot be UTF-8 it seems, so we had to change this
> to ISO-8859-1 like:
>
> <?xml version="1.0" encoding="ISO-8859-1"?>
> <!DOCTYPE molecule SYSTEM "cml.dtd">
>
> this works, but UTF-8 does not.
> The Jmol app however doesn't care either way.
>
> J. Long
> New Products and Math Modeling
> The Dow Chemical Company
> South Charleston, WV 25303
> Office: 304.747.4919
>
> > ----------
> > From: Bradley A. Smith[SMTP:br...@ba...]
> > Sent: Sunday, May 13, 2001 7:55 PM
> > To: jmo...@li...
> > Subject: Re: [Jmol-developers] cml in jmol applet
> >
> > Thanks, Charlie, for pointing out this problem.
> >
> > The problem was a defect in the ReaderFactory. The ReaderFactory
attempts
> > to
> > determine the input file type based upon the file contents. For CML, it
> > was
> > requiring that the document type with the "cml.dtd" be declared on the
> > second line. For the next version, this restriction will be lifted, and
it
> > will be assumed that any file with the first line starting as "<?xml"
will
> > be a CML file.
> >
> > Until the next version, any CML files should contain the following as
> > their
> > first two lines:
> > <?xml version="1.0"?>
> > <!DOCTYPE molecule SYSTEM "cml.dtd">
> >
> > Thanks,
> >   Bradley
> >
> >
> > ----- Original Message -----
> > From: "Fulton CR (Charles)" <ful...@uc...>
> > To: <jmo...@li...>
> > Sent: Thursday, May 10, 2001 9:37 AM
> > Subject: [Jmol-developers] cml in jmol applet
> >
> >
> > > The following cml displays fine in the Jmol application. However, it
> > will
> > > not display inside of JmolApplet. Just checking to see if my syntax
was
> > > correct. We are using the applet downloaded from the site.
> > >
> > > <?xml version="1.0" encoding="UTF-8"?>
> > > <molecule>
> > > <atomArray>
> > >     <stringArray builtin="elementType">O C H H H H </stringArray>
> > >     <floatArray builtin="x3">-1.824 -0.764 -1.372 -0.143 -0.143 -1.233
> > > </floatArray>
> > >     <floatArray builtin="y3">0.842 -0.219 1.790 -0.112 -0.112 -1.202
> > > </floatArray>
> > >     <floatArray builtin="z3">-0.000 -0.000 -0.000 -0.890 0.890 -0.000
> > > </floatArray>
> > >   </atomArray>
> > > </molecule>
> > >
> > >
> > > thanks,
> > >
> > > -charlie.
> > >
> > >
> > >
> > >
>
> --------------------------------------------------------------------------
> > --
> > > ------
> > > Charles Fulton
> > > Platforms Team
> > > Information Research Development & Infrastructure
> > > The Dow Chemical Company
> > > S. Charleston, WV
> > > phone: 304.747.3175
> > >
>
> --------------------------------------------------------------------------
> > --
> > > ------
> > >
> > > _______________________________________________
> > > Jmol-developers mailing list
> > > Jmo...@li...
> > > http://lists.sourceforge.net/lists/listinfo/jmol-developers
> > >
> >
> >
> > _______________________________________________
> > Jmol-developers mailing list
> > Jmo...@li...
> > http://lists.sourceforge.net/lists/listinfo/jmol-developers
> >
>
> _______________________________________________
> Jmol-developers mailing list
> Jmo...@li...
> http://lists.sourceforge.net/lists/listinfo/jmol-developers
>

RE: [Jmol-developers] cml in jmol applet

[Long JW (John) <lo...@uc...>]

In Charlie's example code:

> <?xml version="1.0" encoding="UTF-8"?>
> 
There is also an issue with the encoding.
In our testing, adding the first two lines you mention is not enough. If the
encoding is present, it cannot be UTF-8 it seems, so we had to change this
to ISO-8859-1 like:

<?xml version="1.0" encoding="ISO-8859-1"?>
<!DOCTYPE molecule SYSTEM "cml.dtd">

this works, but UTF-8 does not.
The Jmol app however doesn't care either way.

J. Long
New Products and Math Modeling
The Dow Chemical Company
South Charleston, WV 25303
Office: 304.747.4919

> ----------
> From: 	Bradley A. Smith[SMTP:br...@ba...]
> Sent: 	Sunday, May 13, 2001 7:55 PM
> To: 	jmo...@li...
> Subject: 	Re: [Jmol-developers] cml in jmol applet
> 
> Thanks, Charlie, for pointing out this problem.
> 
> The problem was a defect in the ReaderFactory. The ReaderFactory attempts
> to
> determine the input file type based upon the file contents. For CML, it
> was
> requiring that the document type with the "cml.dtd" be declared on the
> second line. For the next version, this restriction will be lifted, and it
> will be assumed that any file with the first line starting as "<?xml" will
> be a CML file.
> 
> Until the next version, any CML files should contain the following as
> their
> first two lines:
> <?xml version="1.0"?>
> <!DOCTYPE molecule SYSTEM "cml.dtd">
> 
> Thanks,
>   Bradley
> 
> 
> ----- Original Message -----
> From: "Fulton CR (Charles)" <ful...@uc...>
> To: <jmo...@li...>
> Sent: Thursday, May 10, 2001 9:37 AM
> Subject: [Jmol-developers] cml in jmol applet
> 
> 
> > The following cml displays fine in the Jmol application. However, it
> will
> > not display inside of JmolApplet. Just checking to see if my syntax was
> > correct. We are using the applet downloaded from the site.
> >
> > <?xml version="1.0" encoding="UTF-8"?>
> > <molecule>
> > <atomArray>
> >     <stringArray builtin="elementType">O C H H H H </stringArray>
> >     <floatArray builtin="x3">-1.824 -0.764 -1.372 -0.143 -0.143 -1.233
> > </floatArray>
> >     <floatArray builtin="y3">0.842 -0.219 1.790 -0.112 -0.112 -1.202
> > </floatArray>
> >     <floatArray builtin="z3">-0.000 -0.000 -0.000 -0.890 0.890 -0.000
> > </floatArray>
> >   </atomArray>
> > </molecule>
> >
> >
> > thanks,
> >
> > -charlie.
> >
> >
> >
> >
> --------------------------------------------------------------------------
> --
> > ------
> > Charles Fulton
> > Platforms Team
> > Information Research Development & Infrastructure
> > The Dow Chemical Company
> > S. Charleston, WV
> > phone: 304.747.3175
> >
> --------------------------------------------------------------------------
> --
> > ------
> >
> > _______________________________________________
> > Jmol-developers mailing list
> > Jmo...@li...
> > http://lists.sourceforge.net/lists/listinfo/jmol-developers
> >
> 
> 
> _______________________________________________
> Jmol-developers mailing list
> Jmo...@li...
> http://lists.sourceforge.net/lists/listinfo/jmol-developers
> 

Re: [Jmol-developers] cml in jmol applet

[Bradley A. S. <br...@ba...>]

Thanks, Charlie, for pointing out this problem.

The problem was a defect in the ReaderFactory. The ReaderFactory attempts to
determine the input file type based upon the file contents. For CML, it was
requiring that the document type with the "cml.dtd" be declared on the
second line. For the next version, this restriction will be lifted, and it
will be assumed that any file with the first line starting as "<?xml" will
be a CML file.

Until the next version, any CML files should contain the following as their
first two lines:
<?xml version="1.0"?>
<!DOCTYPE molecule SYSTEM "cml.dtd">

Thanks,
  Bradley


----- Original Message -----
From: "Fulton CR (Charles)" <ful...@uc...>
To: <jmo...@li...>
Sent: Thursday, May 10, 2001 9:37 AM
Subject: [Jmol-developers] cml in jmol applet


> The following cml displays fine in the Jmol application. However, it will
> not display inside of JmolApplet. Just checking to see if my syntax was
> correct. We are using the applet downloaded from the site.
>
> <?xml version="1.0" encoding="UTF-8"?>
> <molecule>
> <atomArray>
>     <stringArray builtin="elementType">O C H H H H </stringArray>
>     <floatArray builtin="x3">-1.824 -0.764 -1.372 -0.143 -0.143 -1.233
> </floatArray>
>     <floatArray builtin="y3">0.842 -0.219 1.790 -0.112 -0.112 -1.202
> </floatArray>
>     <floatArray builtin="z3">-0.000 -0.000 -0.000 -0.890 0.890 -0.000
> </floatArray>
>   </atomArray>
> </molecule>
>
>
> thanks,
>
> -charlie.
>
>
>
> --------------------------------------------------------------------------
--
> ------
> Charles Fulton
> Platforms Team
> Information Research Development & Infrastructure
> The Dow Chemical Company
> S. Charleston, WV
> phone: 304.747.3175
> --------------------------------------------------------------------------
--
> ------
>
> _______________________________________________
> Jmol-developers mailing list
> Jmo...@li...
> http://lists.sourceforge.net/lists/listinfo/jmol-developers
>

[Jmol-developers] Use of Jmol in Jude

[Egon W. <eg...@su...>]

Seen the May (#27) issue of Brave GNU World? It seems not be at=20

  http://www.gnu.org/brave-gnu-world/

yet, but i read the German translation in "Linux Magazine"  which is=20
online available at=20

  http://www.linux-magazin.de/ausgabe/2001/06/GNUWorld/gnuworld.html

I mentions Jude, a program develeped by a Spanish PhD student. Take a goo=
d
look at the screenshot :)

And then check out the CVS at SF:

  http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/jude/jude/lib/

Yes, indeed, Jmol rulez!

Have a nice week!

Egon

[Jmol-developers] cml in jmol applet

[Fulton CR (Charles) <ful...@uc...>]

The following cml displays fine in the Jmol application. However, it will
not display inside of JmolApplet. Just checking to see if my syntax was
correct. We are using the applet downloaded from the site. 

<?xml version="1.0" encoding="UTF-8"?>
<molecule>
<atomArray>
    <stringArray builtin="elementType">O C H H H H </stringArray>
    <floatArray builtin="x3">-1.824 -0.764 -1.372 -0.143 -0.143 -1.233
</floatArray>
    <floatArray builtin="y3">0.842 -0.219 1.790 -0.112 -0.112 -1.202
</floatArray>
    <floatArray builtin="z3">-0.000 -0.000 -0.000 -0.890 0.890 -0.000
</floatArray>
  </atomArray>
</molecule>


thanks, 

-charlie.



----------------------------------------------------------------------------
------
Charles Fulton
Platforms Team
Information Research Development & Infrastructure
The Dow Chemical Company
S. Charleston, WV
phone: 304.747.3175
----------------------------------------------------------------------------
------

Re: [Jmol-developers] Tasks for a new release

[Dan G. <gez...@ma...>]

> Therefore, to continue support of a .sea.hqx package, we need a
> volunteer. Any takers?

I can do it.  I'll also figure out what the correct packaging is for
MacOS X.

> Unless someone has a major objection, I would like to adopt this
> scheme, and release a new Jmol as version 1.

Sounds good!


 --Dan

***********************************************************************
  J. Daniel Gezelter
  Assistant Professor                                        Director
  University of Notre Dame                    The OpenScience Project

  gez...@nd...                            gez...@op...
  http://www.nd.edu/~gezelter              http://www.openscience.org
***********************************************************************

[Jmol-developers] Tasks for a new release

[Bradley A. S. <br...@ba...>]

I have noticed that CVS is not tagged for the source files used in =
version 0.6.1 of Jmol. For this reason, I think we should release a new =
version of Jmol. Before releasing a new version, there are several =
matters to address: code for release, packaging, and versioning.


Current state of the code:

Does anyone know a reason why we shouldn't release a version with the =
current source code? Are there any major bugs or features outstanding?


Packaging policy:

Distribution will be allowed in any form of packaging for which a =
developer promises to provide support.

I don't know what the previous policy was, but this policy statement =
stems from Egon's request to have a Debian package. Egon has volunteered =
to create and support one. Therefore, he is the designated Debian =
package maintainer. Hopefully, we will have other volunteers to maintain =
packages for other platforms. If anyone else would like to have a =
certian type of platform-specific package, we should try to find someone =
able to support it. Version 0.6.1 was distributed as .tar.gz, .zip, and =
.sea.hqx package. I am able to create .tar.gz and .zip, but not =
.sea.hqx. Therefore, to continue support of a .sea.hqx package, we need =
a volunteer. Any takers?


Versioning:

I propose a simpler version numbering scheme. Rather than a =
major.minor.patch scheme, I propose a version.patch scheme. This removes =
the vague difference between major and minor release numbers. Each =
release is identified by simply an integer representing the version =
number. The version number is incremented with each release. For =
example, version 1, 2, 3, etc. Most of the time bug fixes should be =
fixed and included in the next release. The only exception to this would =
be when development progress demands branching to implement a bug fix on =
a current release. Then a decimal is added which is incremented for each =
version released from that branch. For example a possible sequence of =
versions might be 1, 1.1, 1.2, 2, 2.1, 3, etc.

Comments?

Unless someone has a major objection, I would like to adopt this scheme, =
and release a new Jmol as version 1.


Thanks,
  Bradley

[Jmol-developers] Build requirements

[Bradley A. S. <br...@ba...>]

Formerly, building Jmol required using GNU make. I have switch the =
project to using Apache Ant, because Ant is a Java build tool which =
requires less project maintenance than make. Ant can be downloaded from =
http://jakarta.apache.org/ant/.

The current requirements for building Jmol are:
  - a Java compiler
  - Ant
  - DocBook XSL stylesheets (available from =
http://www.nwalsh.com/docbook/xsl/)
  - a XSLT tool (Saxon is included in CVS)

The only configuration required before building is specifying the =
location of DocBook by setting the docbook.dir property in the =
build.xml. Alternatively, it can be specified on the command line. For =
example:
    "ant -Ddocbook.dir=3D/usr/lib/sgml/stylesheet/xsl/docbook/nwalsh"

Thanks,
  Bradley

[Jmol-developers] Debian package for Jmol

[E.L. W. <eg...@sc...>]

Hi all,

i am not a Debian developer yet, but in the process and built Debian packages for
Jmol (info below). Debian GNU/Linux is a Linux distribution (http://www.debian.org/).
The package can be downloaded from:

http://www.sci.kun.nl/sigma/Persoonlijk/egonw/jmol/

I would appreciate Debian developers and users testing the package, and welcome
problem reports.

Egon

[Jmol-developers] Overview

[Egon W. <eg...@su...>]

 Hi all,

 I completely lost the overview with the growing number of developers :)
 (not a complaint, i am very happy about it...)

 Could we make an overview of the ongoing programming? Maybe a
 release schedule for the next six months?

 Egon=20
=20

[Jmol-developers] Overview?

[Egon W. <eg...@su...>]

 Hi all,

  I completely lost the overview with the growing number of developers :)
  (not a complaint, i am very happy about it...)

  Could we make an overview of the ongoing programming? Maybe a
  release schedule for the next six months?

  Egon