[Molecuilder-devel] [SCM] MoleCuilder annotated tag v1.4.7 created. v1.4.7

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The annotated tag, v1.4.7 has been created
        at  f64c759050946a7b3803cc35b4665db46d63f8aa (tag)
   tagging  29b35efc972c36f104ccae2ad8b50ce095b475e8 (commit)
  replaces  v1.4.6
 tagged by  Frederik Heber
        on  Thu Aug 21 09:00:02 2014 +0200

- Log -----------------------------------------------------------------
Hydrogen saturation should now work with any atoms, not just up valence of 4.
Added action for structure optimization.
Enabled compilation of molecuilder with Ubuntu 14.04 (gcc48, boost1.55, autoconf 2.6.8, automake 1.11.3).

This version contains the following branches:
29b35ef Candidate_v1.4.7 (distcheck fix, versioning)
0c72e21 Fixes_Ubuntu14_04 (enfored automake option subdir-objects, shared
        libMolecuilder, INCLUDES in Makefile.am deprecated, boost.m4 updated,
        boost::thread fixes)
2cb77c2 VariousFixes (qDebug output in GUI case, fixes to
        CyclicStructureAnalysis))
3a33e3e StructuralOptimization (added ForceAnnealingAction and MakroAction
        StructureOptimizationAction, undo/redo of VerletIntegrationAction)
343c5aa EnhancingHydrogenSaturation (SaturatedFragment rewrite, added
        CorrectBondDegreeAction and SaturationDistanceMaximizer)

Frederik Heber (50):
      TESTFIX: Regression test series Calculations would not run in parallel.
      FIX: CodePatterns_LIBS was introduced in AM_LDFLAGS and not in LIBS.
      FIX: VectorContent::Normalize() did not check for zero factor.
      FIX: Plane's cstor did not check for linear dependence in a numerical stable way.
      FIX: elements db uses wrong hbondangle for degree 1.
      Vector::Is...() functions extended for numeric threshold.
      Removed molecule::AddHydrogenReplacement() and BreadthFirstSearchAdd.
      SaturatedFragment::AddHydrogenReplacementAtom() uses degree 1 if other is missing.
      Refactored SaturatedFragment::saturate() using list of cut bonds.
      FIX: BondedParticleInfo::BondList is now a typedef.
      Added SaturateFragment()::saturateAtom() replacing all cut bonds at once.
      Added new convenience library libMolecuilderTesselation.
      TESTFIX: extracheck threshold is _relative_ 1e-5.
      FIX: VectorContent::Normalize() had int, not double.
      SaturatedFragment can deal with a global saturation position map.
      Added new Vector::IsParallelTo().
      Added SaturatedBond as container for a "dangling bond" and its saturation hydrogens.
      Added SaturationDistanceMaximizer to determine best alphas for SaturatedBonds.
      FragmentationAction now compiles global saturation positions information.
      Added CorrectBondDegreeAction and fixed Calculation tests.
      Extracted common functions from VerletForceIntegration into AtomicForceManipulator.
      Sorted GlobalListOfActions.
      Extended UndoRedoHelpers.
      Extended VerletIntegrationAction wirth Undo/Redo.
      Added CodeCheck for ensuring testsuite..at's appear in tests/regression/Makefile.am.
      Added ForceAnnealingAction.
      FIX: MolecularDynamicsAction works also without JobMarket.
      Added MakroAction StructureOptimizationAction.
      FIX: CheckOrderAtSite() called PrintAtomMask() with wrong AtomCount.
      Giving the maximum components over all force vectors in ForceAnnealing.
      FIX: PdbParser would write coordinates 4.1000 instead of 5.000.
      MPQCCommandFragmentController supports FragmentationAutomationAction being a Process.
      FIX: QtTimeLine::recieveNotification() checked falsely against AtomObserver.
      Fixes due to update to Ubuntu 14.04.
      FIX: Fixes to Action_impl_python, lacked boost preprocessor includes.
      FIX: ReceiveResultContainer could not find functions from base class.
      FIX: Interfragmenter had iter collision.
      FIX: UnitTestMain placed into convenience libUnitTest.
      FIX: ActionQueue::run() did not use boost::thread::sleep_for() correctly.
      QtGUI prints log to console (qDebug) as well.
      FIX: CyclicStructureAnalysis did not robustly detect all cycles.
      FIX: Fragmentations tests used -I and not --correct-bonddegree in case of pdb files.
      Merge branch 'EnhancingHydrogenSaturation' into stable
      Merge branch 'StructuralOptimization' into stable
      Merge branch 'VariousFixes' into stable
      libMolecuilder is now a shared library.
      FIX: FragmentationAutomationAction did not fail correctly with JobMarket in debug mode.
      DOCU: Updated documentation on Ubuntu 14.04.
      Merge branch 'Fixes_Ubuntu14_04' into stable
      Set version to 1.4.7.

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