molecuilder (1.7.1-1) UNRELEASED; urgency=high * fix very slow Qt UI. * improves Qt UI stability. * updates copyright header on VersionAction. * adds molecule context menu, depending on selection. * tesselated molecules can be selected. * fixed the hover. * updates bond table from STO-3G computations * NOTE: bond table loading required now for several bond-related actions! * selected set of atoms may be computed as a fragment. * python: adds getSelectedAtomCount() -- Frederik Heber Wed, 26 Dec 2025 22:09:00 +0100 molecuilder (1.7.0-1) UNRELEASED; urgency=low Major * saturate (fixes to polyhedra and scaling) and bondify (new) * potentials are first class citizens * proper path from molecule, to automated fragmentation, computation, homologies and finally potential training (and visualizing in the UI). * convenience changes in the UI: bigger icons, context menu in gl view, potential tab with plotting * enhancements to python scripting: numpy compatibility, wait returns status, python3 * works inside jupyter notebooks. * can be deployed to k8s for large-scale computations. * graph6 strings, evaluating stability and chemical space evaluation * more selection actions Minor * switch to simpler kubernetes-aimed worker-server setup (health probes, workers don't register but accessed through load balancer) * potential list shown in UI, new actions to add and remove, also potential curves are plotted in UI * general fixes to potential setup to make them work as compound potentials * undomark action * Undo is again without dialog, undo mark is an extra action now. * context menu (right-click) in gl view to manipulate atoms directly * docker file contained in repo * bondify has undo/redo * switched all python to python3 * graph6 fixes and writing strings * generatePotentialAction generates all combinations * full numpy getter and setter to atom position, velocities, and forces. * saturate action allows for just using outer shell (unocc and occ orbitals, only unocc used for adding hydrogens) * stretch bond falls back to tabled distances for element pairs on zero length * select atom's bond neighbors * select atoms randomly * calculate pair correlation between element and selected atoms. Fixes * corrected units and computation in SaveEnergies, renamed from SaveTemperatures * InputAction will also save that file on exit -- Frederik Heber Wed, 22 Oct 2025 19:13:00 +0100 molecuilder (1.6.1-1) UNRELEASED; urgency=low * Added ChemicalSpaceEvaluator Action to assess stability of all possible molecules that match a given Graph6 string using fragmentation method principles. * Python Interface supports (and recommends using) named parameters. Moreover, save-session will write scripts with named parameters. * GUI displays forces and velocities as additional vectors per atom. * AutomationFragmentationAction checks whether workers are still busy and aborts when all workers have crashed. * JobMarket: is now robust when worker or server is killed by signal. * JobMarket: Added GetNumbersOfWorkerOperation. * ForceAnnealing/StructreOptimization Action can now take the bond graph information into account and significantly speed up optimization up to a factor of 3. * added molecular dynamics and structure optimization integration tests. * FIX: recreated and fixed guicheck tests. * StretchBondAction now takes the bond graph into account. * Added examples test case with many ways of translation atoms, see blog post. * enhanced precision of tremolo format making it the recommended file format to use! * Tremolo file format now supports multiple time steps. * DOCU: Updated userguide on empirical potential using HomologyGraph. * Added SelectAtomByName action. * DOCU: several fixes to userguide. * FIX: GUI again reacts to WorldTime changes, i.e. time slider. * changed email address to sent bug reports to. * Added AtomRandomPerturbation to randomly displace atoms. * DOCU: explained wait() necessity in python scripts. * StepWorldTime now uses a single argument. * FIX: Status messages are now always pushed to log, even when logging is captured in GUI. * RotateToPAS has working undo/redo. * Added RotateAroundBond action for rotating molecule around specific bond. * Added very powerful GeometryObjects to use as any vector object or for simply measuring distances and angles in the GUI. * CodePatterns, fix: Chronos is thread-safe, and protecting Verbosity. * fixes: regression tests ports between 11024 and 19999. * builds on Ubuntu 16.04 * MemDebug is now disabled by default. -- Frederik Heber Fri, 02 Mar 2017 23:45:24 +0100 molecuilder (1.6.0-1) UNRELEASED; urgency=low * Dependent packages CodePatterns, JobMarket, levmar, MPQC(_open), and vmg are now contained in the distribution under ThirdParty packages. * Debian package can be easily created. -- Frederik Heber Fri, 02 Mar 2017 23:45:24 +0100 molecuilder (1.5.4-1) UNRELEASED; urgency=low * initial code for allowing charge grids for long-range calculations to work independently for fragments. * fixes to SaturateBond, now properly working by using full SphericalPointDistribution and combinatorial matching to present bonds. * fragment results can now be parsed and save in extra action, not bound to fragmentationautomation oder analysefragmentresults. * fixed fragmentation on subset of atoms. * QtFragmentList now supports proper sorting. * logview in GUI may be disabled by configure-switch. * fitted partial charges are now stored using save/parse-particle-parameters. * introduced implicit charges. * fragmentation-automation fails when server is not/no longer accessible. * fit-partial-charges fits to currently selected atoms and creates unique particles. * removed parse-tremolo-potentials as is superceded by parse-particle-parameters. -- Frederik Heber Fri, 30 Sep 2016 17:45:24 +0200 molecuilder (1.5.3-1) UNRELEASED; urgency=low * QtGui now crashes only in 1-2% of all regression tests (new record). * we copy all information regarding visual entities and regaring the displayed lists via QtObserved... instances or via central ..Observer entities. -- Frederik Heber Sun, 25 Apr 2016 09:11:24 +0200 molecuilder (1.5.2-1) UNRELEASED; urgency=low * Introduced QtObservedInstanceBoard as clean interface between World and QtGui. * Bugfix to FillRegularGrid. * FitParticleCharge -> FitPartialCharge. -- Frederik Heber Sun, 03 Mar 2016 13:48:57 +0100 molecuilder (1.5.1-1) UNRELEASED; urgency=low * Incorporated libcodepatterns rename and other fixes for debian packaging. * More efficient bounding box in molecule, effectively O(log N). * Enhanced hbond distances with more values and consolidated from optimization calculations. * VMG forces now are also working for the long-range part. * Interdistance now combines couples of fragments till a given order. * Smearing of electronic charge distributions greatly improves electronic long-range component. -- Frederik Heber Sun, 06 Feb 2016 23:16:00 +0100 molecuilder (1.5.0-1) UNRELEASED; urgency=low * Initial Release. * This is my first Debian package. -- Frederik Heber Sun, 09 Aug 2015 21:37:00 +0100