Molsketch / News: Recent posts

The latest version includes some major fixes for crashes when drawing arrows or trying to open or save a file. Further, some minor adjustments were made to properly handle the colors of arrows, molecules, and hint points.
My apologies to all those affected by the crashes.

Fixing a lingering bug where graphical properties (especially color) are not properly taken over when inserting fused rings.

After fixing up the build pipelines for hopefully more frequent releases in the future, 0.8.2 Fluorine-14 contains mostly one small fix for the alignment of icons in the settings dialog.

After quite a while some minor improvements:

• improved handling of color (especially radical electrons)
• Windows build updated to Qt 6.6
• finally saying goodbye to QMake as a build system in favor of CMake

Hoping that with more automation the next release should come sooner.

Unfortunately, I had to spend quite a while updating the code to Qt 6 and also building a release pipeline. Therefore, there are just some minor improvements in 0.8.0, but the atom label rendering received a pretty complete overhaul. This fixes issues like including superscripts in selections.

Unfortunately, there has been a string of issues in building the latest Molsketch version 0.7.3 for Windows. I am not a Windows user myself and building requires a rather elaborate effort on my part for setting up a cross-compilation build chain (also considering that at this point it appears preferable to build with a static Qt library).
At this point, two small issues remain:

• My latest build of OpenBabel seems to require a dynamically linked version of zlib. Luckily, I still have an old build around from Molsketch 0.7.1 that works without this, but it will take some time to figure out and fix the problem.
• When testing the latest 0.7.3 release, it turned out that the Wikidata query no longer works in the Windows build. After some investigation, it seems that the problem is caused by HTTPS URLs. Technically, I could probably also go back to an older version of Qt, but would much prefer to update, especially as this also affects OpenSSL, which did have some security patches in the meantime.... read more

This is only a small release coming out in order to establish an automated build - and publication pipeline.
Some new bond types were added nevertheless.

Edit: see also comments on the Windows build

Quick note: as I will be testing the build pipeline (which includes publishing to SourceForge), there will be some dummy releases coming up.
Generally, It will be safe to ignore all of the subsequent Oxygen (0.7.x) releases. The next relevant releases will be the Fluorine versions (0.8.x).
Apologies for any inconvenience caused.

This is just a small release to fix some issues with the (possibly) renamed *.so/*.dll files after removing Qt5 support. In case you were using Molsketch prior to version 0.7.1, it will ask you to update the corresponding settings at start up.

For Windows users, there will be an online installer, as in version 0.7.1, but this will now reside in a separate folder and not be updated as frequently as Molsketch itself. Updates will instead be made available in the online repository at github from which the installer will fetch them. Just start the installer and select the update option

Unfortunately, there were quite some unintended bugs in the last version (some of them older than that, however), which are being addressed by this version
Saving files and re-opening might have sometimes led to crashes due to inconsistencies in the drawing's data. This should now be fixed in -- if not all -- at least most of the cases
Likewise, copying, cutting, and pasting is more robust now.
The last version prematurely updated some code leading to incompatibilities with older versions of Qt (especially pre-5.14). These older versions should now work again; support for Qt 4, on the other hand is completely removed, as it is doubtful whether that still worked anyway.
Translations should now really work throughout Molsketch (currently supported languages: Chinese, English, German, Greek).
Finally, for Windows, an installer is provided, which will download from a repository hosted at github.... read more

With some improvements and fixes that have accumulated during the last year, it is time for another release.
Changelog:

• New localizations: Greek, German, and Chinese
• Direction of attached hydrogen atoms can be set explicitly by user
• Atom shape can also be a circle instead of a rectangle
• Bitmap export with adjustable resolution
• Support OpenBabel 3
• Fixes for sum formula and molecule tooltip
• Fix clipping of bonds
• Fixed OpenBabel support

Finally, and I apologize for the delays, a new version with quite a few fixes and improvements.
Even the snapshot version, which already had quite a bit of that in it still required some additional fixes, but now it should all be wrapped up. Enjoy!
New features:

• Levels on which items are drawn are accessible; bonds are indicated to cover other bonds if on higher level
• Broken bond indicator with same color as rest of bond
• Show sum formula of molecule during hover and after selection
• Closable wiki query
• Improved performance for drag-and-drop insertion of molecules
• Associated *.msm files with Molsketch
• Fixed crashes after undo/redo (changed linkage between molecule, bonds, atoms)
• Fixed global preferences (accidentally had no effect)
• Fixed number of hydrogens and charge in saving/loading molecules

Since version 0.5.2 unfortunately introduced some rather annoying bugs, I highly recommend using the latest snapshot instead (bugs should be fixed there).

To be more precise: you may experience crashes after undoing a "draw" action (e.g. drawing an additional atom or bond) and then performing another action (it doesn't really matter what you do, the point is that the "draw" action is undone and then something else is done).... read more

Ok, Version 0.6.0 announced in the last post is now actually 0.5.2, but it does include a make-over of the drawing settings and the way mouse hovering is treated (note: the "Preferences" have moved from the edit - to the file menu). Enjoy!

Just to get this out of the pipeline: a minor update!
New features:

• alignment tools
• Newman diameter of an atom (so that an atom can be drawn as a plain circle to produce a Newman projection)

Fixes:

• MIME types (Thanks to Alexander Ploumistos at https://sourceforge.net/p/molsketch/bugs/19/)
• Catching exceptions thrown by OpenBabel to avoid program crashes

Version 0.6.0 will include a complete make-over of drawing settings.

After the issues with both the AppImage and the Windows version seem to be under control, it's time to release the next version of Molsketch. Notable new features include the ability to query Wikidata for molecular structures (well, InChI strings, that is -- requires OpenBabel) and support for explicit lone pairs and radical electrons. Enjoy!

Edit (next morning fixes): there's been a minor fix related to https://sourceforge.net/p/molsketch/bugs/17/#e600/e66b/bd49/53a1/9277, which is not essential if the code is working for you as is. Sorry for the inconvenience.

After a long struggle, mainly with external libraries, there is now an AppImage and there is also support for importing molecules from Wikidata.
On my test virtual machine (Ubuntu 14.04), I did encounter some problems using this latter functionality (wikidata) in the AppImage, as it doesn't seem to like some of the OpenBabel formats and in particular not the InChI format. On my real machine (OpenSuSE 42.2), it did work, however. I'll try building an AppImage with an older CentOS next...... read more

Currently, I'm experimenting with providing an AppImage as a more easy-to-run version for the Linux platform. This will include OpenBabel and thus also for its various file formats. The Windows static build should also be enriched with OpenBabel in order to provide im- and exports.

Additionally, I've been experimenting with Wikidata, the interface to Wikipedia's data, to retrieve SMILES strings, from which one can in turn generate molecular formula drawings (via OpenBabel).... read more

For version 0.4.2 (or 0.5, for that matter), I'm planning on performing some clean-ups, so some functionality may go missing. The reason for this is that the code in question has become somewhat unwieldy and does not quite comply with the behavior of the remainder of the program.

Plugins, for instance, have been riddled with bugs, which I inadvertently introduced after making some changes to other parts of the program. In 0.3.0, for instance, inserting a plugin might lead to crashes. At any rate, they were never properly saved to files. Reading them from a file should have worked, but was obviously never really tested.... read more

... and we finally got a text tool. As it uses Qt's facilities, all sorts of formatting are in principle supported, but for now you'll have to copy formatted text from another application into the text field.

On a side note, the cmake build now offers the option to turn off OpenBabel support, which was previously only possible with qmake.
And the legacy stereo bonds (from files created with versions prior to Lithium) are now imported correctly.

With a few fixes and a few extensions, it did seem necessary to release a new version. Be warned: there is still lots of work to be done. For now, some major restructuring tasks have been undertaken: the tests have been extracted into a separate project on GitHub and the molecule library has been decommissioned. Instead, you may now build your own fairly easily. This feature is bound to be improved, however.

Unfortunately, version 0.3.1 contains a few rather nasty and severe bugs, which apparently escaped my inspection. Hence, it is probably preferable to use the next version's snapshot instead for the time being. There is still some work that will go into re-activating the molecule library in that particular version.

Any volunteer help in testing and finding out bugs do not make it into the final version is greatly appreciated!

After a long while, a little update. The main new feature are "decorations", which can be frames, brackets, or the like and will become more flexible in the future.
Also, some improvements have been implemented for arrows (reaction - as well as mechanism arrows). Stay tuned for more...

After some renovation on the code, a new version of Molsketch is ready (although, obviously, there still remain bugs and issues to be fixed).
Notable changes include (but are not limited to):

• native XML format (*.msk)
• right mouse button no longer deletes atoms or bonds (used for context menu instead)
• Qt5 and qmake support (Qt4 and cmake are only checked sporadically. cmake support will continue, Qt4 may fade)
• several minor clean-ups of the user interface
• more consistent undo-support

Molsketch 0.2.0 is the first release since development was taken up again a few months ago. While there are many improvements over 0.1.1, some bugs and imperfections are still there. The long term goal is to have an extendible 2D chemistry application.

The source package can be downloaded from sourceforge.net:
https://sourceforge.net/projects/molsketch/files/
There is also a windows zip file with a version build using Qt's SDK