Petition zum Erhalt und Fortbestand der Professur für Technische Chemie an der TU Dresden

In eigener Sache bitte ich Kenner, ehemalige Studenten und Sympathisanten des Instituts für Technische Chemie Dresden um Unterstützung bei der Petition zum Erhalt und Fortbestand der einzigen Professur für Technische Chemie an der TU Dresden. Da ich selber in der Vergangenheit sehr eng mit dieser Professur (und mittelständischen Unternehmen) zusammen gearbeitet habe, waren die Ereignisse (PDF) der letzten Jahre überraschend für mich. Ich kann mir eine Technische Universität ohne die Professur kaum vorstellen.

Link zur Petition

Packages removed from the debian.wgdd.de repository

Several packages have been removed from the archive:

CDK

The »Chemistry Development Kit« (CDK) now has been officially packaged and uploaded by Michael Koch. If you still have my packages installed, first uninstall/purge libcdk-java-doc, cdk und libcdk-java-dirbrowser (completely) and then install the current version of libcdk-java. Scripts found in cdk will probably be added to the Debian distribution soon.

Jchempaint

Jchempaint has been merged into CDK some time ago and there are plans to build/package it for Debian. My packages were just outdated. Please expect updated packages from the Debian mirror next to you :)

Jmol

Ditto. We are working on an official Debian package. I'm not planning nor working on an official Debian package. But there is an ITP (#512930) for it.

MOLDEN

This package was outdated. The current release is version 4.6. The packaging files have been moved to the debichem groups SVN. You can build the package yourself by using svn-buildpackage. Just download the MOLDEN source and the packaging files. Then set the configuration option svn-override=buildArea for svn-buildpackage to the place where the upstream tarball resists (create the symlink molden_4.6.orig.tar.gz -> molden4.6.tar.gz) and run svn-buildpackage with your preferred options.

We are currently not allowed to distribute MOLDEN binaries or its source with the Debian distribution. But we are in contact with upstream.

clamassassin

There is an official clamassassin Debian package for some time now. However, the package only ships the clamssassin script, but not clamdassassin.

Gabedit, DRAWxtl and libint are on their way into Debian

This is an information for all those users and developers, which are interested in chemistry and computational chemistry packages in Debian: As part of the debichem project at Alioth, I recently added Gabedit, DRAWxtl and libint to our project SVN repository. All packages are in a fairly good state for an upload into the Debian NEW queue. Today we (Michael Banck and me) began with gabedit. The other packages will follow soon (I swear).

Also thanks to Abdul-Rahman Allouche, Larry Finger (and the other DRAWxtl authors) and Edward Valeev for these software packages and their response to my mails :)

Our SVN repository further contains Debian packaging files for the MOLDEN software package. Unfortunately we are currently not allowed to ship the MOLDEN source or binaries within Debian. However, you can use our SVN repository to build the package for yourself. Just install the svn-buildpackage package, download the MOLDEN source tarball and our SVN (wnpp/molden/), configure svn-buildpackage for this setup (a complete how-to will follow soon) and then build the package by running svn-buildpackage.

If you are interested in our work and/or if you want to help, subscribe to our mailing list and meet us there.

Let file(1) recognize a chemical MIME type - the next level

As written earlier, the file command may detect chemical MIME types, if you feed its database with the necessary definition rules. Now check out the cmd.magic.mime file and run the file command with

$ file -m cmd.magic.mime -i your_test_file.ext

for one or more chemical files. The detection is limited to chemical MIME types, that have magic pattern in the chemical-mime-data database.

The file cmd.magic.mime was created via XSLT conversion of the original chemical-mime-data database and can be used for KDE and file(1). One of the following package releases (probably 0.1.95) will provide it.

Update

Unfortunately this magic.mime file cannot be used for KDE. As pointed out by David Faure, KDE uses an older syntax that doesn't know e.g. the search type. So I have to find another solution for KDE or wait for better days.

Let file(1) recognize a chemical MIME type

Ok, it's 8 o'clock in the morning and I need some sleep. But first let's show you some small example, how to detect chemical MIME types with the file(1) command. Put the following stuff into your /etc/magic (the local magic data configuration file for the file(1) command):

0               string          VjCD0100                CDX binary file
>8              belong          0x04030201
>>12            bequad          0x0000000000000000
>>>20           beshort         0x0000
>>>>34          string          ChemDraw                written with ChemDraw
>>>>>42         string          x                       b%.4s
>>>>22          beshort         0x0080                  (new format)
>>>>22          beshort         0x0000                  (old format)

Now search for a CDX (ChemDraw binary) file and run the file command:

$ find . -name "*.cdx" -exec file "{}" ";"
./example.cdx: data (that's really broken)
./dummy.cdx: lif file (that's a CACTVS file in reality)
./x-chemdraw/structures25-27.cdx: CDX binary file written with ChemDraw 4.5 (old format)
./x-chemdraw/structures96-101.cdx: CDX binary file written with ChemDraw 4.5 (old format)
./x-chemdraw/structures40-48.cdx: CDX binary file written with ChemDraw 4.5 (old format)
./x-chemdraw/dimethylamine.cdx: CDX binary file written with ChemDraw 7.0 (old format)
./x-chemdraw/dimethylaminesimple.cdx: CDX binary file (old format)
./x-chemdraw/untitled.cdx: CDX binary file written with ChemDraw 8.0 (new format)
./x-chemdraw/structures1-12.cdx: CDX binary file written with ChemDraw 4.5 (old format)

Why I do this? The chemical-mime-data package contains magic pattern, that can be used to automatically create the rules for the file command too, so file(1) can determine the chemical MIME type too. Expect a stylesheet to extract this information from the database soon.

And now I will get some sleep.

Update

And here, how to recognize the MIME type. Add the following to /etc/magic.mime:

0               string          VjCD0100
>8              belong          0x04030201
>>12            bequad          0x0000000000000000
>>>20           beshort         0x0000
>>>>22          beshort         0x0080                  chemical/x-cdx
>>>>22          beshort         0x0000                  chemical/x-cdx

and run the file(1) command with the -i switch:

$ find . -name "*.cdx" -exec file -i "{}" ";"
./example.cdx: application/octet-stream
./dummy.cdx: application/octet-stream
./x-chemdraw/structures25-27.cdx: chemical/x-cdx
./x-chemdraw/structures96-101.cdx: chemical/x-cdx
./x-chemdraw/structures40-48.cdx: chemical/x-cdx
./x-chemdraw/dimethylamine.cdx: chemical/x-cdx
./x-chemdraw/dimethylaminesimple.cdx: chemical/x-cdx
./x-chemdraw/untitled.cdx: chemical/x-cdx
./x-chemdraw/structures1-12.cdx: chemical/x-cdx

And now I really get some sleep. Cheerio!

chemical-mime-data 0.1.94 released

Today I released a new version of the chemical-mime-data package, namely 0.1.94. This version adds and improves support for various chemical MIME types (see below). It fixes several build issues and improves some detection and build stuff. The RH bug #225095 (SF.net bug #1616568) has been fixed. The TODO list is now also a little bit shorter, because several items (source and package documentation) have been done with this release too.

This version adds support for:

• chemical/x-cactvs-ascii
• chemical/x-cactvs-binary
• chemical/x-cactvs-table
• chemical/x-cdxml
• chemical/x-gamess-output
• chemical/x-gulp
• chemical/x-ncbi-asn1
• chemical/x-ncbi-asn1-binary
• chemical/x-ncbi-asn1-xml

Support has been improved for:

• chemical/x-cdx
• chemical/x-cml
• chemical/x-cif
• chemical/x-dmol
• chemical/x-gamess-input
• chemical/x-gaussian-input
• chemical/x-gaussian-log
• chemical/x-genbank
• chemical/x-hin
• chemical/x-inchi
• chemical/x-inchi-xml
• chemical/x-mdl-rxnfile
• chemical/x-mmcif
• chemical/x-mol2
• chemical/x-msi-car
• chemical/x-msi-hessian
• chemical/x-msi-mdf
• chemical/x-msi-msi
• chemical/x-pdb
• chemical/x-shelx

The full release changelog can found at the SF.net project site.

An updated Debian package will be available soon in the experimental tree (not in sid because of the release freeze).

Chemistry packages accepted in Debian

I'm proud to announce, that chemical MIME was accepted by the Debian FTP-masters and it is now part of the Debian distribution as package chemical-mime-data . However the GNOME chemistry utils are not yet accepted, but they are awaiting the review by the FTP-masters in the NEW-queue. The next packages will be gchempaint (probably 0.6.7) and bkchem (probably 0.11.5).

The Debian packaging files of these packages are officially maintained by the debichem Alioth project members (I belong to this group too) and they can be found in our SVN repository. I have to say "Many thanks!" to Michael Banck, my sponsor, and "Join us!" to all, who want to help packaging.

I've updated the Debian Wiki to fit the new situation. Search there, of you want to know, which packages await an review to suggest them for Debian officially.

Stay tuned.

Next RC 0.1.93 for chemical-mime-data delayed

Because of issues and changes inside the sourceforge.net CVS infrastructure, it will need a few more days, before I can release the next RC for chemical-mime-data, which will be version 0.1.93. There are still a few steps to go for release 0.2.0, but we are on the way.

First official chemical-mime-data release 0.1.92

Today I released the first official version of chemical-mime-data after moving back to sourceforge.net. This release is thought to be the first RC for the upcoming 0.2.0 version. I made massive changes since our last release of chemicalMIME 2. One important improvement is IMHO the database, which is now the place to drop all informations. Have a look at the release notes to get an overview, what has changed.