A tragic loss has hit the open source software community. Warren Lyford DeLano, among other things, open source advocate, scientist and the author of the famous PyMOL molecular visualization system, suddenly passed away at the age of 37. I remember you as a genial, pleasent intelligent guy and software author. It has been a pleasure to work with you. Good bye.
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 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.
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 attached 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 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.
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!
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:
Support has been improved for:
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).
I’m proud to announce, that chemical-mime-data was accepted by the Debian FTP-masters and it is now part of the Debian distribution. 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. 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.
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.
Stay tuned and regards, Daniel
Today I released the first official version of chemical-mime-data after moving away and 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.
Enjoy (and report bugs to me), Daniel