Sciurus' Blog

Time for another update report on molsKetch Helium.

Thanks to some patches of Tim Vandermeersch, the previews in the library are working again (and are much faster now) and the atom labels are now printed in the correct order. Mandatory screenshots:

Also moving is working again and implicit hydrogens are now included when the document is saved.

The current focus is on improving the charge and implicit hydrogen heuristics and a new style of drawing bonds. More news will follow.

As promised an update on the progress on molsKetch Helium over the past two weeks. There aren't that many interesting things to mention, but I hope it's worth reading.

I've been working on splitting off the most reusable part of molsKetch in a library, to make use in 3rd party apps easier. I'm not completely sure in how many parts I should split it. Just one big libmolsketch? Or a dedicated part for the molecule stuff (libmol?) and the drawing stuff (libsketch?) ? For the moment I'll stick with the big one. I've run in some problems linking the application to a shared version of the library, so the SVN version will link staticly by default. Also having a separate library should make building the KPart a little more sane.

Furthermore, I've been running some test on saving and loading document in molsKetch to eliminate any regressions since the last release. There are still a number of issues to be solved. The most obivious is the preservation of the different bond types. Certain formats in OpenBabel seem to ignore the SetWedge() and SetHash() functions (while there is support in the formats as far as I know), so the orientation of the bonds is not preserved.

Finally I've updated the site of molsKetch with some new screenshots. The blog software my provider is using is ancient, the reason of the horrible quality of the thumbnails. The full versions shouldn't be a problem. Perhaps I should move the gallery to a more suitable location. My mailbox is open for any nice live-actions shots of molsKetch.

Stay tuned for further updates...

Far too late, but I've just made an alpha version of molsKetch Helium available on SourceForge. For the brave of you who want to try it: just follow the instructions in the INSTALL file. It should work with Qt 4.3, CMake 2.4 and OpenBabel 2.1. If you encounter a not-so-obvious bug or have other suggestions and feedback, just let me know in the SourceForge bug-tracker or by mail. Also check the release notes or TODO file for known issues.

Highlights are:

• An improved periodic table
• New panel for quick access to often used draw settings
• An initial KPart version (requires KDE4)
• Initial support for rotating
• Font and bondwidth can now be changed
• Support for i18n

The file can be downloaded here.

Thanks for all the fan-mail, it boosts motivation. There were some suggestions about more regular updates of the progress. Perhaps it's an idea to make regular blog postings on the progress, say once every two weeks or so. The posts won't be that interesting, but at least you'll be able to follow the progress (without continues svn checks). I'm open for other suggestions.

Time to bring some life to this blog.

Progress on the new version is not going as fast as I was hoping, so I've decided to postpone the new architecture to Lithium and backport as many features as possible to the old architecture for Helium as possible. Also, this will allow me to take more time for some good rethinking of the internals of molsKetch.

I hope to have an alpha version of Helium on-line in a few weeks, so stay tuned for more info on which features are going to make it and which are not.

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)

The first release candidate for molsKetch Deuterium is available. Please give it a try and report any bugs and other problems. If no major issues arise, I'll release the final by the end of the week.

You can find the release candidate here: http://downloads.sourceforge.net/molsketch/molsketch-0.1.1deuterium-rc1.tar.gz

molsKetch has found a new home on SourceForge: http://molsketch.sourceforge.net.

Of course there is also a project page with downloads, access to the code and a bug tracker. This will give me the opportunity to host all things on a central location, use the SourceForge File Release System and use Subversion to access the code. I hope that this will mean spending more time on improving molsKetch and less time on administrative issues.

This also means that all bugs, feature requests and problems can now be reported on the SourceForge tracker.

Thanks to Markus Bongard (ATG), molsKetch Hydrogen is now running on MacOSX (screenshot). What a lovely sight...

A package (only for Intel Macs for now) can be found here.

After almost six months of development molsKetch Hydrogen is finally there. This first release will give you all you need to draw 2D molecular structures. molsKetch has several functions helping you to draw a consistant structure quickly and easily. After you've finished your molecule, you can save it in all the formats supported by OpenBabel or export it as picture for further use in other documents. Regular used molecules can be saved in the built-in library for further use.

Of course there is still much room for improvement, but basic functionality is available. For an overview of the features click here. Screenshots can be found here.

For the Debian users out there: I've prepared a package for Sid, so you're free to give it a try. Other users can compile from source for the moment. Dependencies are Qt 4.2 and OpenBabel 2.

Unfortunately, I still wasn't able to link molsKetch against OpenBabel on Windows, so open/save is disabled for the moment. This doesn't mean it's entirely useless under Windows, as you can still copy/export molecules in several graphical formats.

molsKetch is released under the GPL and can be downloaded for free with the folowing links:

• molsKetch Hydrogen for Windows (.exe)
• molsKetch Hydrogen for Debian Sid (.deb)
• molsKetch Hydrogen source (.tar.gz)

As with the previous versions, I'm open for new ideas and suggestions. Also please report any bugs or problems you encounter. I'll do my best to fix them.

Het is zo ver: de eerste betaversie van molsKetch is uit. Ten opzichte van de laatste alpha zijn er weer veel dingen verbeterd en toegevoegd. Als de laatste bugs van deze versie geplet zijn, zal de final uitkomen.

Mochten er tijdens het testen problemen tegenkomen of mocht iets niet werken, laat het dan even weten in de comments hieronder. Ook dingen die nog ontbreken of andere ideeën zijn welkom. Nuttige feedback wordt beloond met een vermelding in het programma.

De enige bekende beperking onder Windows is momenteel het opslaan en openen van bestanden. Dit door een probleem met de OpenBabel bibliotheek.

De versie voor Windows is beschikbaar onder deze link. De broncode voor andere besturingssystemen is hier te vinden.

Na veel geploeter heb ik de eerste versie voor Windows aan de praat gekregen. Het programma is nog lang niet af en er zijn dus nog voldoende bugs en ontbrekende features om mij nog even bezig te houden. Maar uiteraard zijn alle problemen, commentaar en ideeën van harte welkom.

De problemen die sowieso nog in deze versie zitten:

• er kunnen geen documenten geopend of opgeslagen worden
• bij het verplaatsen van onderdelen treden er vreemde bijverschijnselen op en crasht het programma

Verder ben ik vooral benieuwd of het programma goed installeert en of het überhaupt wel draait in de grote boze buitenwereld. Dat het programma bij mij installeert en werkt zonder schadelijke bijwerkingen, wil niet zeggen dat dat elders ook zo is. Hierover (in het bijzonder de schadelijke bijwerkingen) kan ik dus geen garanties leveren.

Voor de geïnteresseerde: de alphaversie voor Windows is op deze plek te downloaden. De gebruikers onder linux (en mogelijke andere systemen) zullen de broncode voorlopig nog zelf moeten compileren. Zorg er dan voor dat Qt4 en de OpenBabel bibliotheek al geïnstalleerd zijn.