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ParseTremoloPotentials is gone, as it is superseded by ParseParticleParameters which is also responsible for parsing partial charges.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