We added some more complex code for saturating atoms properly. It takes fully into account already present bonds and tries to match to internally stored SphericalPointDistributions as best as possible. This gives really good initial results, i.e. building up molecules just by adding a few carbon, nitrogens and oxygens, when subsequent structure optimization relaxes everything to its proper equilibrium positions.

Moreover, we fixed the fragmentation working on just a subset of atoms, i.e. leaving out saturation water.

In the GUI, the Fragment list can now be properly sorted (and still clicked to get the fragment as set of selected atoms).

FragmentationAutomation will actually fail when the Server is unreachable and not spin forever.

ParseTremoloPotentials is gone, as it is superseded by ParseParticleParameters which is also responsible for parsing partial charges. See also SaveParticleParameters.

Note that for versions in between this and v1.5.0 we refrained from producing debian packages as these did not really bring any good change for the user. Starting from this version, it is again worth to update ... especially with what's coming up!

1.5.3? Where is 1.5.1 and 1.5.2?!

To make things clear from the start, it took quite some effort to produce a clean interface between the GUI and the rest of molecuilder. Hence, v1.5.1 and v1.5.2 are sort of versions in between.

v1.5.3 basically brings mostly internal changes in form of the QtObservedInstanceBoard, namely all of the information about atoms, molecules, ... required for visual representation are copied and updated as needed. This is to make sure that things just live long enough for the sloppy GUI.

Right now, 1% of all test cases do not work in case of using the GUI as promised with v1.5.0.

Apart from that we have:

• The FitParticleCharge action is renamed to FitPartialCharge.
• long range forces working when using vmg.
• interdistance option when using Fragmentation action allows now to combine fragments up to a given order.
• electronic charges are additionally smeared for long-range electrostatic calculations which improves accuracy.

It is done!

From this version onward we provide debian packages (Ubuntu 12.04) for convenience to the user. Please note that MoleCuilder depends on several other packages, three of which had to be manually compiled and are made available at DownloadRedistribution. Especially, Qt3D was quite hard to get to work.

Furthermore, the GUI is now thread-safe!

Qt works with threads, MoleCuilder so far did not. Sure this had to clash. Now, the interface between MoleCuilder and the GUI done with Qt has been secured with mutexes and clean structures and the GUI is safe for use. All the more because it is contained in the debian package. Have fun fooling around with it.

Note that there still might be some issues. True stable execution will probably come up with v1.5.1 but early-adopters are welcome to try it out. For the moment 1 percent of all guicheck testsuite tests (see last versions about that) are still allowed to fail.

We need to switch from ​Codepatterns v1.2.9 to CodePatterns v1.3.0. Most of the GUI tests are failing because of race conditions in the code. CodePatterns v1.3.0 brings the Observer/Observable up to multi-threaded speed by having mutexes in place.

Hence, in this version nothing is really changed but we only switch underlying library versions on a version update.

Prepare for v1.5.0 because then the GUI tests will be working.

This is a smaller update that will some time later make a difference.

First of all, a new action has been added that allows saturating any present atom, i.e. creating methane is as simple as adding a carbon atom and saturating it.

Second, we finally have something like a testsuite for the GUI which should bring this interface up to a usable level real soon. The tests are mostly failing but this should soon be corrected.

Last, some GUI stuff has been fixed and enhanced such as the info boxes that now reveal a bit more about the atom or molecule the mouse pointer is hovering over.