Sciurus' Blog

After almost two months of development, molsKetch Deuterium is available for download. This is an in between release of molsKetch (hence the name) containing mostly bug fixes. Most of the work is visible under the hood in the source code. End-users will only notice the support for OpenBabel under Windows (you can now load, save and import documents) and few other changes like deleting items with the right mouse button and the new lay-out for the element table. For a more extensive list of changes, see the changelog.

Looking forward to the next release of molsKetch, Helium, a few changes will occur. The next release will be most likely depending on Qt 4.3 and OpenBabel 2.1. With the new releases of these great frameworks, molsKetch will have a tighter integration of OpenBabel and better support for SVG. Some features I've in mind for Helium are (3D) rotating of molecules, support for different drawing styles for molecules and a built-in SMILES prompt.

As always, I'm open for any suggestions and other feedback. Please report any bugs or other problems at the bug tracker on sourceforge.net page.

You can download molsKetch Deuterium from the SourceForge page:

• molsKetch Deuterium for Microsoft Windows (.exe)
• molsKetch Deuterium for Debian Sid (.deb)
• molsKetch Deuterium Source (.tar.gz)

To anybody looking for the distribution-specific packages - Gentoo ebuild for MolsKetch lives here: http://bugs.gentoo.org/show_bug.cgi?id=178156

Hi Harm,

interested in meeting up in Eindhoven some day? I am there regularly...

Egon

Oh, and please check out the programmeerzomer.nl, which might finance further molsKetch development.

Bond angles which are intuitive
For a title such as "bond angle" its reasonable to assume it is the angle increments for the drawing and not the divisor in the sum 360/x.

The ability to rotate a selection by 22.5 degree increments would also be useful, if bonds where preserved during this it would be helpful also.

Also saving a file does not assign the file extension you select you have to manually input it.

@Josh Thanks for the suggestions. I guess you already added them to the tracker. Expect some of these improvements in the next release.

@Egon Interesting initiative programmeerzomer.nl. Didn't know of it's existence. Too bad I'm needed at my work all summer.

I have had a thought on the periodic table 'problem', chemists will find it a lot easier to use if it resembles the standard layout in the standard orientation (as on http://www.webelements.com/) rather than flipped horizontally and rotated 90 degrees. If the periodic table were at the bottom of the screen with a tab which opened and closed the full view of it, it would be very easy to use. Upon closing the full view it could display the commonly used elements.

In regards to 3d would you consider collaborating with:

Kalzium's 3D viewer google summer of code project:
http://edu.kde.org/kalzium/news.php#itemStudenttoworkonKalziums3DMolecularEditorduringGSoC2007

or

Avogadro
http://www.kde-apps.org/content/show.php/Avogadro?content=59521

This would save on duplication efforts if the code could be transferable/useful.

@Josh I'm in contact with the Avogadro guys and trying to avoid duplicated effort. One of the ideas is to use libavogadro for 3D viewing in molsKetch. As far as I now Kalzium's 3D viewer also uses libavogadro.

Sciurus, my GSoC student would like to use molsKetch in his project to find documents that mention a certain molecule, so molsKetch as input tool, but was unable to compile it. His blog is at http://neksa.blogspot.com/

I am conducting research on the effects of deuterium as a chemotherapy on cancer patients and other illnessess. Can you help!

Deuterium is just the release name of molsKetch. So, I'm afraid I can't help you there.

Just downloaded your program and have been trying it out and looking at the source code. It looks very nice so far, though it seems to be in the fairly early stage. I look forward to subsequent features and releases. In particular, I currently do not see a way to adjust the position of an existing atom in a way that snaps to the grid, correct?

One thing you might consider is to extract the generic structure representations and operations into a separate C++ library, decoupled from the Qt code. If you could do that, you might perhaps provide a very valuable and important niche for the development of open source 2D chemical structure editors. I've looked around a little and have failed to find any existing C++ libraries that do this. I'd be happy to collaborate on that, if you're interested.

hii

Thanks for your information, i have read it, very good!