KryoMol and copy/paste chemistry on KDE

Dear Armando,

I am porting some of the KryoMol stuff to Kalzium, mainly
ThumbnailCreator and
the KFilePlugin stuff, I will send you patches on monday
A question that I am worrying about is mimetypes, I think we should

Speaking of MIME types, I’d love to see some shared clipboard types
for Qt/KDE applications. Right now, Avogadro is copying graphics, XYZ
coordinates as text (in the selection buffer), and MDL Molfile for
the QClipboard.

Does this seem like a reasonable start, e.g. chemistry/x-mdl-molfile
to copy/paste across different chemistry apps on KDE? It would be
nice if molsketch, KryoMol, Avogadro… could all share data this way.

Cheers,
-Geoff

This will be nice of course, now KryoMol implements copy/paste through
clipboard quite efficently.
Main problem is quantum chemistry files since they dont have, in most
cases, specific extensions. What KryoMol does is to guess the file
type by contents. I am not very sure if a kind of MimeMagic could be
written from my code. I will ask on KDE list how KMimeMagic exactly
works in KDE4.

A thing that I would consider very important for Kalzium is the
management of Chime based webpages. Currently Kryomol has basic code
for managment of some chime scripting. I think that it would be a
very desirable aim that Kalzium could render chime pages. Besides, it
would be possilbe to extend the current chime system to other type of
files ( displaying vibrations orbitals etc. )

Wishes
Armando

Dear Armando,

I am porting some of the KryoMol stuff to Kalzium, mainly
ThumbnailCreator and
the KFilePlugin stuff, I will send you patches on monday
A question that I am worrying about is mimetypes, I think we should

Speaking of MIME types, I’d love to see some shared clipboard types for
Qt/KDE applications. Right now, Avogadro is copying graphics, XYZ
coordinates as text (in the selection buffer), and MDL Molfile for the
QClipboard.

Does this seem like a reasonable start, e.g. chemistry/x-mdl-molfile to
copy/paste across different chemistry apps on KDE? It would be nice if
molsketch, KryoMol, Avogadro… could all share data this way.

Cheers,
-Geoff

On May 13, 2007, at 11:52 AM, qoajnv@usc.es wrote:

A thing that I would consider very important for Kalzium is the
management of Chime based webpages. Currently Kryomol has basic
code for managment of some chime scripting. I think that it would
be a very desirable aim that Kalzium could render chime pages.
Besides, it would be possilbe to extend the current chime system to
other type of files ( displaying vibrations orbitals etc. )

I think it’s important to allow interactive scripting like Chime too.
But I think Jmol has started to become the de facto standard for this
too:
http://jmol.sourceforge.net/scripting/
http://jmol.sourceforge.net/docs/

So I think if we wanted to have this sort “chime script support,” we
should look at what Jmol has done.

Cheers,
-Geoff

On May 13, 2007, at 11:52 AM, qoajnv@usc.es wrote:

This will be nice of course, now KryoMol implements copy/paste
through clipboard quite efficently.
Main problem is quantum chemistry files since they dont have, in
most cases, specific extensions. What KryoMol does is to guess the
file type by contents. I am not very sure if a kind of MimeMagic
could be written from my code. I will ask on KDE list how
KMimeMagic exactly works in KDE4.

The Chemical MIME project is gathering some “magic mime” data too.
http://chemical-mime.sourceforge.net/

I suspect they would be happy to help with improving chemistry MIME
detection and “magic” as well. They have some already, but you may be
able to contribute others.

Cheers,
-Geoff

Am Sonntag, den 13.05.2007, 12:33 -0400 schrieb Geoffrey Hutchison:

On May 13, 2007, at 11:52 AM, qoajnv@usc.es wrote:

This will be nice of course, now KryoMol implements copy/paste
through clipboard quite efficently.
Main problem is quantum chemistry files since they dont have, in
most cases, specific extensions. What KryoMol does is to guess the
file type by contents.

KDE has an own database for this purpose based on file’s magic.mime
database. However, QM input files do often not follow a special syntax
and so, they are hard to recognize. But maybe you want to try the
current results?

I am not very sure if a kind of MimeMagic
could be written from my code. I will ask on KDE list how
KMimeMagic exactly works in KDE4.

The Chemical MIME project is gathering some “magic mime” data too.
http://chemical-mime.sourceforge.net/

I support KDE3 with content pattern and .desktop files and KDE4 uses the
shared-mime-info database, which I use as base for the project. KDE3
support realization has a few problems: See
http://lists.kde.org/?l=kde-core-devel&m=117179551506286&w=2 to read
more about it. Issues are: Same extensions need the
X-KDE-PatternsAccuracy=50 key/value. The used file/libmagic version does
not support regex/search types, so it’s almost impossible to realize the
start_offset:end_offset shared-mime-info syntax in KDE3. file/libmagic
(any version, not only KDE3) do not support masked strings.

I suspect they would be happy to help with improving chemistry MIME
detection and “magic” as well. They have some already, but you may be
able to contribute others.

Yes, I appreciate all contributions to improve these pattern. Please
have a look at http://chemical-mime.sourceforge.net (especially the
linked overview in 4.).

Please recognize the general problem: chemical is NOT a registered MIME
primary type and the RfC for registering chemical is not active anymore.
I’m currently writing on some more detailed documentation, but it’s not
yet ready.

Regards, Daniel