Changeset 7c7c4a

Timestamp:

Feb 12, 2016, 11:15:04 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

2831b3

Parents:

e25448

git-author:

Frederik Heber <heber@…> (10/16/15 11:51:16)

git-committer:

Frederik Heber <heber@…> (02/12/16 23:15:04)

Message:

FIX: All ObservedValue's of GLMoleculeObject_atom/bond/molecule wrapped into vector.

• the idea is that a GLMoleculeObject may only remove itself _after_ each and every contained Observer has gotten the subjectKilled() signal from the Observables. Only then will destroying the Object and its members thereby not cause any signOff() which try to access Observables or their channels which are no longer present. This can be imagined as a graph where we have to start destroying object at the very bottom.
• This is the avoid the following conflict: A superior object gets note of a molecule to be removed. It sends the visual representation a signal to remove itself, which causes it to use signOff(). On a parallel track (in another thread) we have the observed object calling subjectKilled() to inform any Observer about its immediate destruction. These two tracks collide. Now, we let first pass all subjectKilled() and when the last Observable has gotten its signal, we begin destroying the visual rep.
• rerouted signal/slots accordingly.

Location:

src/UIElements

Files:

• Makefile.am (modified) (1 diff)
• Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) (14 diffs)
• Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) (3 diffs)
• Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) (9 diffs)
• Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) (3 diffs)
• Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) (22 diffs)
• Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) (3 diffs)
• Views/Qt4/Qt3D/GLWorldScene.cpp (modified) (15 diffs)
• Views/Qt4/Qt3D/GLWorldScene.hpp (modified) (1 diff)
• Views/Qt4/Qt3D/GLWorldView.cpp (modified) (2 diffs)
• Views/Qt4/Qt3D/ObservedValue_wCallback.hpp (added)

src/UIElements/Makefile.am

@@ -225 +225 @@
         UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp \
         UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.hpp \
+  UIElements/Views/Qt4/Qt3D/ObservedValue_wCallback.hpp \
   UIElements/Views/Qt4/QDebugStream.hpp
 

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp

@@ -57 +57 @@
 #include "WorldTime.hpp"
 
+#include "ObservedValue_wCallback.hpp"
+
 using namespace boost::assign;
 
@@ -80 +82 @@
   Observer(std::string("GLMoleculeObject_atom")+toString(_id)),
   atomref(getAtom(_id)),
-  AtomIndex(
-      atomref,
-      boost::bind(&GLMoleculeObject_atom::updateIndex, this),
-      "AtomIndex_"+toString(_id),
-      _id,
-      AtomIndexChannels),
-  AtomPosition(
-      atomref,
-      boost::bind(&GLMoleculeObject_atom::updatePosition, this),
-      "AtomPosition_"+toString(_id),
-      updatePosition(),
-      AtomPositionChannels),
-  AtomElement(
-      atomref,
-      boost::bind(&GLMoleculeObject_atom::updateElement, this),
-      "AtomElement"+toString(_id),
-      updateElement(),
-      AtomElementChannels),
-  AtomBonds(
-      atomref,
-      boost::bind(&GLMoleculeObject_atom::updateBonds, this),
-      "AtomBonds_"+toString(_id),
-      updateBonds(),
-      AtomBondsChannels),
+  ObservedValues(MAX_ObservedTypes),
+  subjectKilledCount(0),
   owner(NULL)
 {
+  initObservedValues(_id);
+
   setObjectId(_id);
   resetPosition();
@@ -154 +136 @@
 {
   deactivateObserver();
+  destroyObservedValues();
 }
 
 void GLMoleculeObject_atom::resetIndex()
 {
-  const atomId_t newId = AtomIndex.get();
+  const atomId_t newId = getAtomIndex();
   const size_t oldId = objectId();
   ASSERT( newId != oldId,
@@ -170 +153 @@
 void GLMoleculeObject_atom::resetPosition()
 {
-  const Vector Position = AtomPosition.get();
+  const Vector Position = getAtomPosition();
   LOG(4, "INFO: GLMoleculeObject_atom::resetIndex() - new position is "+toString(Position)+".");
   setPosition(QVector3D(Position[0], Position[1], Position[2]));
@@ -179 +162 @@
   size_t elementno = 0;
   const element * const _type = World::getInstance().
-      getPeriode()->FindElement(AtomElement.get());
+      getPeriode()->FindElement(getAtomElement());
   if (_type != NULL) {
     elementno = _type->getAtomicNumber();
@@ -205 +188 @@
 void GLMoleculeObject_atom::resetBonds()
 {
-  ListOfBonds_t ListOfBonds_new = AtomBonds.get();
+  ListOfBonds_t ListOfBonds_new = getAtomBonds();
   std::sort(ListOfBonds_new.begin(), ListOfBonds_new.end());
   ListOfBonds_t BondsToAdd;
@@ -220 +203 @@
       iter != BondsToAdd.end();
       ++iter) {
-    const GLMoleculeObject_bond::SideOfBond side = (iter->first == AtomIndex.get()) ?
+    const GLMoleculeObject_bond::SideOfBond side = (iter->first == getAtomIndex()) ?
         GLMoleculeObject_bond::left : GLMoleculeObject_bond::right;
     emit BondsAdded(iter->first, iter->second, side);
@@ -259 +242 @@
 void GLMoleculeObject_atom::wasClicked()
 {
-  LOG(4, "INFO: GLMoleculeObject_atom: atom " << AtomIndex.get() << " has been clicked");
-  emit clicked(AtomIndex.get());
+  LOG(4, "INFO: GLMoleculeObject_atom: atom " << getAtomIndex() << " has been clicked");
+  emit clicked(getAtomIndex());
 }
 
@@ -283 +266 @@
 Vector GLMoleculeObject_atom::updatePosition() const
 {
-  const atom * const _atom = getAtom(AtomIndex.get());
+  const atom * const _atom = getAtom(getAtomIndex());
   if (_atom != NULL) {
     return _atom->getPosition();
@@ -293 +276 @@
 atomicNumber_t GLMoleculeObject_atom::updateElement() const
 {
-  const atom * const _atom = getAtom(AtomIndex.get());
+  const atom * const _atom = getAtom(getAtomIndex());
   if (_atom != NULL) {
     return _atom->getElementNo();
@@ -304 +287 @@
 {
   ListOfBonds_t ListOfBonds;
-  const atom * const _atom = getAtom(AtomIndex.get());
+  const atom * const _atom = getAtom(getAtomIndex());
   if (_atom != NULL) {
     // make sure position is up-to-date
@@ -315 +298 @@
           (*iter)->rightatom->getId()) );
   } else {
-    ELOG(2, "Atom with id "+toString(AtomIndex.get())+" is already gone.");
+    ELOG(2, "Atom with id "+toString(getAtomIndex())+" is already gone.");
   }
   return ListOfBonds;
@@ -328 +311 @@
 {
   deactivateObserver();
+
+  countsubjectKilled();
 }
 
@@ -357 +342 @@
     ASSERT(0, "GLMoleculeObject_atom::recieveNotification() - received notification from unexpected source.");
 }
+
+void GLMoleculeObject_atom::countsubjectKilled()
+{
+  ++subjectKilledCount;
+
+  if (subjectKilledCount > ObservedValues.size())
+    emit InstanceRemoved(getAtomIndex());
+}
+
+void GLMoleculeObject_atom::initObservedValues(const atomId_t _id)
+{
+  // fill ObservedValues
+  boost::function<void()> subjectKilled =
+      boost::bind(&GLMoleculeObject_atom::countsubjectKilled, this);
+  ObservedValues[AtomIndex] = new ObservedValue_wCallback<atomId_t>(
+      atomref,
+      boost::bind(&GLMoleculeObject_atom::updateIndex, this),
+      "AtomIndex_"+toString(_id),
+      _id,
+      AtomIndexChannels,
+      subjectKilled);
+  ObservedValues[AtomPosition] = new ObservedValue_wCallback<Vector>(
+      atomref,
+      boost::bind(&GLMoleculeObject_atom::updatePosition, this),
+      "AtomPosition_"+toString(_id),
+      updatePosition(),
+      AtomPositionChannels,
+      subjectKilled);
+  ObservedValues[AtomElement] = new ObservedValue_wCallback<atomicNumber_t>(
+      atomref,
+      boost::bind(&GLMoleculeObject_atom::updateElement, this),
+      "AtomElement"+toString(_id),
+      updateElement(),
+      AtomElementChannels,
+      subjectKilled);
+  ObservedValues[AtomBonds] = new ObservedValue_wCallback<ListOfBonds_t>(
+      atomref,
+      boost::bind(&GLMoleculeObject_atom::updateBonds, this),
+      "AtomBonds_"+toString(_id),
+      updateBonds(),
+      AtomBondsChannels,
+      subjectKilled);
+}
+
+void GLMoleculeObject_atom::destroyObservedValues()
+{
+  delete boost::any_cast<ObservedValue_wCallback<atomId_t> *>(ObservedValues[AtomIndex]);
+  delete boost::any_cast<ObservedValue_wCallback<Vector> *>(ObservedValues[AtomPosition]);
+  delete boost::any_cast<ObservedValue_wCallback<atomicNumber_t> *>(ObservedValues[AtomElement]);
+  delete boost::any_cast<ObservedValue_wCallback<ListOfBonds_t> *>(ObservedValues[AtomBonds]);
+  ObservedValues.clear();
+}
+
+atomId_t GLMoleculeObject_atom::getAtomIndex() const
+{
+  return boost::any_cast<ObservedValue_wCallback<atomId_t> *>(ObservedValues[AtomIndex])->get();
+}
+
+Vector GLMoleculeObject_atom::getAtomPosition() const
+{
+  return boost::any_cast<ObservedValue_wCallback<Vector> *>(ObservedValues[AtomPosition])->get();
+}
+
+atomicNumber_t GLMoleculeObject_atom::getAtomElement() const
+{
+  return boost::any_cast<ObservedValue_wCallback<atomicNumber_t> *>(ObservedValues[AtomElement])->get();
+}
+
+GLMoleculeObject_atom::ListOfBonds_t GLMoleculeObject_atom::getAtomBonds() const
+{
+  return boost::any_cast<ObservedValue_wCallback<ListOfBonds_t> *>(ObservedValues[AtomBonds])->get();
+}

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp

@@ -15 +15 @@
 
 #include "GLMoleculeObject.hpp"
+
+#include <vector>
+#include <boost/any.hpp>
 
 #include "CodePatterns/ObservedValue.hpp"
@@ -61 +64 @@
   void elementChanged();
   void bondsChanged();
+  void InstanceRemoved(const atomId_t);
 
 private:
@@ -88 +92 @@
   atom * const atomref;
 
-  //!> cached value of the atom's id
-  ObservedValue<atomId_t> AtomIndex;
-  //!> cached value of the atom's position
-  ObservedValue<Vector> AtomPosition;
-  //!> cached value of the atom's element
-  ObservedValue<atomicNumber_t> AtomElement;
-  //!> cached value of the atom's id
-  ObservedValue<ListOfBonds_t> AtomBonds;
+private:
+  /** Observed Values **/
+
+  //!> enumeration of observed values to match with entries in ObservedValues
+  enum ObservedTypes {
+    //!> contains the current atom index
+    AtomIndex,
+    //!> contains the current atom position
+    AtomPosition,
+    //!> contains the current atom element
+    AtomElement,
+    //!> contains the current set of bonds atoms fort the atom
+    AtomBonds,
+    //!> gives the size of the enumeration
+    MAX_ObservedTypes
+  };
+
+  //!> vector with all observed values
+  std::vector<boost::any> ObservedValues;
+
+  /** Initializes all \a ObservedValues entries.
+   *
+   * \param _id atom id
+   */
+  void initObservedValues(const atomId_t _id);
+
+  /** Destroys all \a ObservedValues entries.
+   *
+   */
+  void destroyObservedValues();
+
+  /** Getter to atom index contained in \a ObservedValues.
+   *
+   * \return atom's index
+   */
+  atomId_t getAtomIndex() const;
+
+  /** Getter to atom position contained in \a ObservedValues.
+   *
+   * \return atom's position
+   */
+  Vector getAtomPosition() const;
+
+  /** Getter to atom element contained in \a ObservedValues.
+   *
+   * \return atom's elemnt
+   */
+  atomicNumber_t getAtomElement() const;
+
+  /** Getter to atom bonds contained in \a ObservedValues.
+   *
+   * \return atom's bonds
+   */
+  ListOfBonds_t getAtomBonds() const;
+
+  /** Counts how many ObservedValues got subjectKilled.
+   *
+   * This is used to give InstanceRemoved() signal only when each and every
+   * ObservedValue (and the instance itself) has been subjectKilled by the
+   * monitored Observable. Only then can we safely remove the instance.
+   *
+   */
+  void countsubjectKilled();
+
+  //!> counts how many ObservedValues have already been subjectKilled()
+  mutable size_t subjectKilledCount;
+
+private:
 
   //!> list of channels when index needs to update

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp

@@ -57 +57 @@
 #include "World.hpp"
 
+#include "ObservedValue_wCallback.hpp"
+
 
 // static entities
@@ -82 +84 @@
   bondowner(getAtom(leftatomId)->getBond(getAtom(rightatomId)).get()),
   BondSide(side),
-  leftPosition(
-      leftowner,
-      boost::bind(&GLMoleculeObject_bond::updateLeftPosition, this),
-      "BondleftPosition_"+toString(leftatomId),
-      updateLeftPosition(),
-      BondPositionChannels),
-  rightPosition(
-      rightowner,
-      boost::bind(&GLMoleculeObject_bond::updateRightPosition, this),
-      "BondrightPosition_"+toString(rightatomId),
-      updateRightPosition(),
-      BondPositionChannels),
-  leftElement(
-      leftowner,
-      boost::bind(&GLMoleculeObject_bond::updateLeftElement, this),
-      "BondleftElement"+toString(leftatomId),
-      updateLeftElement(),
-      BondElementChannels),
-  rightElement(
-      rightowner,
-      boost::bind(&GLMoleculeObject_bond::updateRightElement, this),
-      "BondrightElement"+toString(rightatomId),
-      updateRightElement(),
-      BondElementChannels),
-  Degree(
-      bondowner,
-      boost::bind(&GLMoleculeObject_bond::updateDegree, this),
-      "BondDegree"+toString(leftatomId)+"_"+toString(rightatomId),
-      updateDegree(),
-      BondDegreeChannels),
+  ObservedValues(MAX_ObservedTypes),
+  subjectKilledCount(0),
   leftobservable_enabled(false),
   rightobservable_enabled(false)
 {
+  initObservedValues();
+
   // sign on as observer (obtain non-const instance before)
   bondowner->signOn(this, BondObservable::BondRemoved);
@@ -141 +117 @@
   // signOff() if not already done
   removeChannels();
+  destroyObservedValues();
 }
 
@@ -170 +147 @@
 }
 
-void GLMoleculeObject_bond::removeMe()
-{
-  // sign off
-  emit BondRemoved(leftatomId, rightatomId);
-}
-
 void GLMoleculeObject_bond::update(Observable *publisher)
 {
@@ -185 +156 @@
   // we signOff from all other sources
   removeChannels();
-  // then indicate to remove us
-  removeMe();
+  // check whether we should be removed
+  countsubjectKilled();
 }
 
@@ -278 +249 @@
 void GLMoleculeObject_bond::resetElement()
 {
-  size_t elementno = rightElement.get();
+  size_t elementno = getrightElement();
   QGLMaterial *elementmaterial = getMaterial(elementno);
   setMaterial(elementmaterial);
@@ -285 +256 @@
 void GLMoleculeObject_bond::resetWidth()
 {
-  const double factor = 1.0f+.5f*(Degree.get()-1);
+  const double factor = 1.0f+.5f*(getDegree()-1);
   LOG(2, "DEBUG: GLMoleculeObject_bond::resetWidth() - setting bond's width to " << factor << ".");
   setScaleX(factor);
@@ -295 +266 @@
 void GLMoleculeObject_bond::resetPosition()
 {
-  Vector Position = leftPosition.get();
-  Vector OtherPosition = rightPosition.get();
+  Vector Position = getleftPosition();
+  Vector OtherPosition = getrightPosition();
   const double distance =
       Position.distance(OtherPosition)/2.;
@@ -346 +317 @@
   return _atom;
 }
+
+void GLMoleculeObject_bond::countsubjectKilled()
+{
+  ++subjectKilledCount;
+
+  if (subjectKilledCount > ObservedValues.size())
+    emit BondRemoved(leftatomId, rightatomId);
+}
+
+void GLMoleculeObject_bond::initObservedValues()
+{
+  // fill ObservedValues
+  boost::function<void()> subjectKilled =
+      boost::bind(&GLMoleculeObject_bond::countsubjectKilled, this);
+  ObservedValues[leftPosition] = new ObservedValue_wCallback<Vector>(
+      leftowner,
+      boost::bind(&GLMoleculeObject_bond::updateLeftPosition, this),
+      "BondleftPosition_"+toString(leftatomId),
+      updateLeftPosition(),
+      BondPositionChannels,
+      subjectKilled);
+  ObservedValues[rightPosition] = new ObservedValue_wCallback<Vector>(
+      rightowner,
+      boost::bind(&GLMoleculeObject_bond::updateRightPosition, this),
+      "BondrightPosition_"+toString(rightatomId),
+      updateRightPosition(),
+      BondPositionChannels,
+      subjectKilled);
+  ObservedValues[leftElement] = new ObservedValue_wCallback<atomicNumber_t>(
+      leftowner,
+      boost::bind(&GLMoleculeObject_bond::updateLeftElement, this),
+      "BondleftElement"+toString(leftatomId),
+      updateLeftElement(),
+      BondElementChannels,
+      subjectKilled);
+  ObservedValues[rightElement] = new ObservedValue_wCallback<atomicNumber_t>(
+      rightowner,
+      boost::bind(&GLMoleculeObject_bond::updateRightElement, this),
+      "BondrightElement"+toString(rightatomId),
+      updateRightElement(),
+      BondElementChannels,
+      subjectKilled);
+  ObservedValues[Degree] = new ObservedValue_wCallback<int>(
+      bondowner,
+      boost::bind(&GLMoleculeObject_bond::updateDegree, this),
+      "BondDegree"+toString(leftatomId)+"_"+toString(rightatomId),
+      updateDegree(),
+      BondDegreeChannels,
+      subjectKilled);
+}
+
+void GLMoleculeObject_bond::destroyObservedValues()
+{
+  delete boost::any_cast<ObservedValue_wCallback<Vector> *>(ObservedValues[leftPosition]);
+  delete boost::any_cast<ObservedValue_wCallback<Vector> *>(ObservedValues[rightPosition]);
+  delete boost::any_cast<ObservedValue_wCallback<atomicNumber_t> *>(ObservedValues[leftElement]);
+  delete boost::any_cast<ObservedValue_wCallback<atomicNumber_t> *>(ObservedValues[rightElement]);
+  delete boost::any_cast<ObservedValue_wCallback<int> *>(ObservedValues[Degree]);
+  ObservedValues.clear();
+}
+
+Vector GLMoleculeObject_bond::getleftPosition() const
+{
+  return boost::any_cast<ObservedValue_wCallback<Vector> *>(ObservedValues[leftPosition])->get();
+}
+
+Vector GLMoleculeObject_bond::getrightPosition() const
+{
+  return boost::any_cast<ObservedValue_wCallback<Vector> *>(ObservedValues[rightPosition])->get();
+}
+
+atomicNumber_t GLMoleculeObject_bond::getleftElement() const
+{
+  return boost::any_cast<ObservedValue_wCallback<atomicNumber_t> *>(ObservedValues[leftElement])->get();
+}
+
+atomicNumber_t GLMoleculeObject_bond::getrightElement() const
+{
+  return boost::any_cast<ObservedValue_wCallback<atomicNumber_t> *>(ObservedValues[rightElement])->get();
+}
+
+int GLMoleculeObject_bond::getDegree() const
+{
+  return boost::any_cast<ObservedValue_wCallback<int> *>(ObservedValues[Degree])->get();
+}

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp

@@ -15 +15 @@
 
 #include "GLMoleculeObject.hpp"
+
+#include <vector>
+#include <boost/any.hpp>
 
 #include "CodePatterns/Observer/Observer.hpp"
@@ -70 +73 @@
 
 private:
-  /** This must be called from subjectKilled() only.
-   *
-   * We remove from all other Observables in a controlled manner.
-   *
-   * removeBond(), and removeChannels() must have been called before (or one of
-   * the subjects has been killed).
-   *
-   */
-  void removeMe();
   void removeChannels();
 
@@ -105 +99 @@
   const enum SideOfBond BondSide;
 
-  ObservedValue<Vector> leftPosition;
-  ObservedValue<Vector> rightPosition;
-  ObservedValue<atomicNumber_t> leftElement;
-  ObservedValue<atomicNumber_t> rightElement;
-  ObservedValue<int> Degree;
+
+private:
+  /** Observed Values **/
+
+  //!> enumeration of observed values to match with entries in ObservedValues
+  enum ObservedTypes {
+    //!> contains the position of the left atom
+    leftPosition,
+    //!> contains the position of the right atom
+    rightPosition,
+    //!> contains the element of the left atom
+    leftElement,
+    //!> contains the element of the right atom
+    rightElement,
+    //!> contains the degree of the bond
+    Degree,
+    //!> gives the size of the enumeration
+    MAX_ObservedTypes
+  };
+
+  //!> vector with all observed values
+  std::vector<boost::any> ObservedValues;
+
+  /** Initializes all \a ObservedValues entries.
+   *
+   */
+  void initObservedValues();
+
+  /** Destroys all \a ObservedValues entries.
+   *
+   */
+  void destroyObservedValues();
+
+  /** Getter to left atom's position contained in \a ObservedValues.
+   *
+   * \return left atom's position
+   */
+  Vector getleftPosition() const;
+
+  /** Getter to right atom's position contained in \a ObservedValues.
+   *
+   * \return right atom's position
+   */
+  Vector getrightPosition() const;
+
+  /** Getter to left atom's element contained in \a ObservedValues.
+   *
+   * \return left atom's element
+   */
+  atomicNumber_t getleftElement() const;
+
+  /** Getter to rightatom's element contained in \a ObservedValues.
+   *
+   * \return right atom's element
+   */
+  atomicNumber_t getrightElement() const;
+
+  /** Getter to bond's degree contained in \a ObservedValues.
+   *
+   * \return bond's degree
+   */
+  int getDegree() const;
+
+  /** Counts how many ObservedValues got subjectKilled.
+   *
+   * This is used to give InstanceRemoved() signal only when each and every
+   * ObservedValue (and the instance itself) has been subjectKilled by the
+   * monitored Observable. Only then can we safely remove the instance.
+   *
+   */
+  void countsubjectKilled();
+
+  //!> counts how many ObservedValues have already been subjectKilled()
+  mutable size_t subjectKilledCount;
+
+private:
 
   //!> indicate whether we are signed in to leftobservable

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp

@@ -63 +63 @@
 #include "Atom/TesselPoint.hpp"
 #include "World.hpp"
+
+#include "ObservedValue_wCallback.hpp"
 
 using namespace boost::assign;
@@ -122 +124 @@
       boost::bind(&GLMoleculeObject_molecule::updateAtoms, this)
       ),
-  MolIndex(
-      molref,
-      MolIndexUpdater,
-      "MoleculeIndex_"+toString(_molid),
-      _molid,
-      IndexChannels),
-  MolName(
-      molref,
-      MolNameUpdater,
-      "MoleculeName_"+toString(_molid),
-      updateName(),
-      NameChannels),
+  ObservedValues(MAX_ObservedTypes),
+  subjectKilledCount(0),
   TesselationHull(
       molref,
@@ -139 +131 @@
       "MoleculeTesselationHull_"+toString(_molid),
       HullChannels),
-  BoundingBox(
-      molref,
-      BoundingBoxUpdater,
-      "MoleculeBoundingBox_"+toString(_molid),
-      initBoundingBox(),
-      BoundingBoxChannels),
-  PresentAtoms(
-      molref,
-      PresentAtomsUpdater,
-      "MoleculeAtoms_"+toString(_molid),
-      updateAtoms(),
-      AtomsChannels),
   hoverAtomId(-1)
 {
+  initObservedValues(_molid);
+
   setObjectId(_molid);
   setMaterial(getMaterial(1));
@@ -199 +181 @@
       boost::bind(&GLMoleculeObject_molecule::updateAtoms, this)
       ),
-  MolIndex(
-      molref,
-      MolIndexUpdater,
-      "MoleculeIndex_"+toString(_molid),
-      _molid,
-      IndexChannels),
-  MolName(
-      molref,
-      MolNameUpdater,
-      "MoleculeName_"+toString(_molid),
-      updateName(),
-      NameChannels),
+  ObservedValues(MAX_ObservedTypes),
+  subjectKilledCount(0),
   TesselationHull(
       molref,
@@ -216 +188 @@
       "MoleculeTesselationHull_"+toString(_molid),
       HullChannels),
-  BoundingBox(
-      molref,
-      BoundingBoxUpdater,
-      "MoleculeBoundingBox_"+toString(_molid),
-      initBoundingBox(),
-      BoundingBoxChannels),
-  PresentAtoms(
-      molref,
-      PresentAtomsUpdater,
-      "MoleculeAtoms_"+toString(_molid),
-      atoms_t(),
-      AtomsChannels),
   hoverAtomId(-1)
 {
+  initObservedValues(_molid);
+
   setObjectId(_molid);
   setMaterial(getMaterial(1));
@@ -254 +216 @@
 {
   deactivateObserver();
+  destroyObservedValues();
 }
 
@@ -270 +233 @@
 {
   // sign on as observer (obtain non-const instance before)
-  const molecule * const _molecule = getMolecule(MolIndex.get());
+  const molecule * const _molecule = getMolecule(getMolIndex());
   if (_molecule != NULL) {
     owner = static_cast<const Observable *>(_molecule);
@@ -278 +241 @@
     owner->signOn(this, molecule::IndexChanged);
   } else {
-    ELOG(1, "GLMoleculeObject_molecule() - added null object for not present mol id " << MolIndex.get());
+    ELOG(1, "GLMoleculeObject_molecule() - added null object for not present mol id " << getMolIndex());
   }
 
@@ -332 +295 @@
   QGeometryData geo;
 
-  const molecule * const molref = getMolecule(MolIndex.get());
+  const molecule * const molref = getMolecule(getMolIndex());
   if (molref == NULL) {
-    ELOG(1, "Could not createMoleculeMesh, molecule with id " << MolIndex.get() << " already gone.");
+    ELOG(1, "Could not createMoleculeMesh, molecule with id " << getMolIndex() << " already gone.");
     return geo;
   }
@@ -353 +316 @@
 
   // we need at least three points for tesselation
-  if (PresentAtoms.get().size() >= 3) {
+  if (getPresentAtoms().size() >= 3) {
     // Tesselate the points.
     Tesselation T;
-    PointCloudAdaptor<molecule> cloud(const_cast<molecule *>(molref), MolName.get());
+    PointCloudAdaptor<molecule> cloud(const_cast<molecule *>(molref), getMolName());
     T(cloud, minradius);
 
@@ -413 +376 @@
 molecule::BoundingBoxInfo GLMoleculeObject_molecule::updateBoundingBox() const
 {
-  return BoundingBox.get();
+  return getBoundingBox();
 }
 
 GLMoleculeObject_molecule::atoms_t GLMoleculeObject_molecule::updateAtoms()
 {
-  const molecule * const mol = getMolecule(MolIndex.get());
+  const molecule * const mol = getMolecule(getMolIndex());
   if (mol != NULL) {
     const atomId_t id = mol->lastChangedAtomId();
@@ -436 +399 @@
 std::string GLMoleculeObject_molecule::updateName() const
 {
-  const molecule * const mol = getMolecule(MolIndex.get());
+  const molecule * const mol = getMolecule(getMolIndex());
   return mol->getName();
 }
@@ -448 +411 @@
 void GLMoleculeObject_molecule::resetBoundingBox()
 {
-  molecule::BoundingBoxInfo info = BoundingBox.get();
+  molecule::BoundingBoxInfo info = getBoundingBox();
   setPosition(QVector3D(info.position[0], info.position[1], info.position[2]));
   setScale(info.radius + 0.3); // getBoundingSphere() only sees atoms as points, so make the box a bit bigger
@@ -455 +418 @@
 void GLMoleculeObject_molecule::resetAtoms()
 {
-  const atoms_t atoms = PresentAtoms.get();
+  const atoms_t atoms = getPresentAtoms();
   std::vector<atomId_t> InsertedAtoms;
   std::vector<atomId_t> RemovedAtoms;
@@ -479 +442 @@
 void GLMoleculeObject_molecule::resetIndex()
 {
-  const atomId_t newId = MolIndex.get();
+  const atomId_t newId = getMolIndex();
   const size_t oldId = objectId();
   ASSERT( newId != oldId,
@@ -544 +507 @@
   // remove owner: no more signOff needed
   owner = NULL;
+
+  countsubjectKilled();
 }
 
 void GLMoleculeObject_molecule::recieveNotification(Observable *publisher, Notification_ptr notification)
 {
-  const molecule * const _molecule = getMolecule(MolIndex.get());
+  const molecule * const _molecule = getMolecule(getMolIndex());
   // when molecule is NULL we will soon get destroyed anyway
   if (_molecule == NULL)
@@ -556 +521 @@
 #ifdef LOG_OBSERVER
     observerLog().addMessage() << "++ Update of Observer "<< observerLog().getName(static_cast<Observer *>(this))
-          << " received notification from molecule " << MolIndex.get() << " for channel "
+          << " received notification from molecule " << getMolIndex() << " for channel "
           << notification->getChannelNo() << ".";
 #endif
@@ -577 +542 @@
         observerLog().addMessage() << "++ Observer " << observerLog().getName(static_cast<Observer *>(this)) << " received notification that atom "+toString(_id)+" has been removed.";
   #endif
-        emit AtomRemoved(_id);
         emit TesselationHullChanged();
         emit BoundingBoxChanged();
@@ -719 +683 @@
   connect (atomObject, SIGNAL(BondsRemoved(const atomId_t, const atomId_t)), this, SLOT(bondRemoved(const atomId_t, const atomId_t)));
   connect (atomObject, SIGNAL(indexChanged(GLMoleculeObject_atom*, const atomId_t, const atomId_t)), this, SLOT(changeAtomId(GLMoleculeObject_atom*, const atomId_t, const atomId_t)));
+  connect (atomObject, SIGNAL(InstanceRemoved(const atomId_t)), this, SIGNAL(AtomRemoved(const atomId_t)));
 
   if (m_objectId  == -1)
@@ -773 +738 @@
     if (moleculeObject == this){
       // Propagate signal.
-      emit hoverChanged(MolIndex.get(), 0);
+      emit hoverChanged(getMolIndex(), 0);
     }
   }
@@ -871 +836 @@
 void GLMoleculeObject_molecule::wasClicked()
 {
-  LOG(4, "INFO: GLMoleculeObject_molecule: atom " << MolIndex.get() << " has been clicked");
-  emit moleculeClicked(MolIndex.get());
+  LOG(4, "INFO: GLMoleculeObject_molecule: atom " << getMolIndex() << " has been clicked");
+  emit moleculeClicked(getMolIndex());
 }
 
@@ -906 +871 @@
   return mol;
 }
+
+void GLMoleculeObject_molecule::countsubjectKilled()
+{
+  ++subjectKilledCount;
+
+  if (subjectKilledCount > ObservedValues.size())
+    emit InstanceRemoved(getMolIndex());
+}
+
+void GLMoleculeObject_molecule::initObservedValues(const moleculeId_t _molid)
+{
+  // fill ObservedValues
+  boost::function<void()> subjectKilled =
+      boost::bind(&GLMoleculeObject_molecule::countsubjectKilled, this);
+  ObservedValues[MolIndex] = new ObservedValue_wCallback<moleculeId_t>(
+      molref,
+      MolIndexUpdater,
+      "MoleculeIndex_"+toString(_molid),
+      _molid,
+      IndexChannels,
+      subjectKilled);
+  ObservedValues[MolName] = new ObservedValue_wCallback<std::string>(
+      molref,
+      MolNameUpdater,
+      "MoleculeName_"+toString(_molid),
+      updateName(),
+      NameChannels,
+      subjectKilled);
+  ObservedValues[BoundingBox] = new ObservedValue_wCallback<molecule::BoundingBoxInfo>(
+      molref,
+      BoundingBoxUpdater,
+      "MoleculeBoundingBox_"+toString(_molid),
+      initBoundingBox(),
+      BoundingBoxChannels,
+      subjectKilled);
+  ObservedValues[PresentAtoms] = new ObservedValue_wCallback<atoms_t>(
+      molref,
+      PresentAtomsUpdater,
+      "MoleculeAtoms_"+toString(_molid),
+      updateAtoms(),
+      AtomsChannels,
+      subjectKilled);
+}
+
+void GLMoleculeObject_molecule::destroyObservedValues()
+{
+  delete boost::any_cast<ObservedValue_wCallback<moleculeId_t> *>(ObservedValues[MolIndex]);
+  delete boost::any_cast<ObservedValue_wCallback<std::string> *>(ObservedValues[MolName]);
+  delete boost::any_cast<ObservedValue_wCallback<molecule::BoundingBoxInfo> *>(ObservedValues[BoundingBox]);
+  delete boost::any_cast<ObservedValue_wCallback<atoms_t> *>(ObservedValues[PresentAtoms]);
+  ObservedValues.clear();
+}
+
+moleculeId_t GLMoleculeObject_molecule::getMolIndex() const
+{
+  return boost::any_cast<ObservedValue_wCallback<moleculeId_t> *>(ObservedValues[MolIndex])->get();
+}
+
+std::string GLMoleculeObject_molecule::getMolName() const
+{
+  return boost::any_cast<ObservedValue_wCallback<std::string> *>(ObservedValues[MolName])->get();
+}
+
+molecule::BoundingBoxInfo GLMoleculeObject_molecule::getBoundingBox() const
+{
+  return boost::any_cast<ObservedValue_wCallback<molecule::BoundingBoxInfo> *>(ObservedValues[BoundingBox])->get();
+}
+
+GLMoleculeObject_molecule::atoms_t GLMoleculeObject_molecule::getPresentAtoms() const
+{
+  return boost::any_cast<ObservedValue_wCallback<atoms_t> *>(ObservedValues[PresentAtoms])->get();
+}

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp

@@ -17 +17 @@
 
 #include <Qt3D/qgeometrydata.h>
+
+#include <vector>
+#include <boost/any.hpp>
 
 #include "CodePatterns/Cacheable.hpp"
@@ -68 +71 @@
   void AtomRemoved(const atomId_t _id);
   void IdChanged();
+  void InstanceRemoved(const moleculeId_t);
 
 private slots:
@@ -141 +145 @@
   boost::function<atoms_t ()> PresentAtomsUpdater;
 
-  //!> contains the current molecule index
-  ObservedValue<moleculeId_t> MolIndex;
-  //!> contains the current molecule name
-  ObservedValue<std::string> MolName;
+private:
+  /** Observed Values **/
+
+  //!> enumeration of observed values to match with entries in ObservedValues
+  enum ObservedTypes {
+    //!> contains the current molecule index
+    MolIndex,
+    //!> contains the current molecule name
+    MolName,
+    //!> contains newest version of the bounding box on request
+    BoundingBox,
+    //!> contains the current live set of atoms for the molecule
+    PresentAtoms,
+    //!> gives the size of the enumeration
+    MAX_ObservedTypes
+  };
+
+  //!> vector with all observed values
+  std::vector<boost::any> ObservedValues;
+
+  /** Initializes all \a ObservedValues entries.
+   *
+   * \param _moid molecule id
+   */
+  void initObservedValues(const moleculeId_t _molid);
+
+  /** Destroys all \a ObservedValues entries.
+   *
+   */
+  void destroyObservedValues();
+
+  /** Getter to molecule index contained in \a ObservedValues.
+   *
+   * \return molecule's index
+   */
+  moleculeId_t getMolIndex() const;
+
+  /** Getter to molecule name contained in \a ObservedValues.
+   *
+   * \return molecule's name
+   */
+  std::string getMolName() const;
+
+  /** Getter to molecule's bounding box contained in \a ObservedValues.
+   *
+   * \return molecule's bounding box
+   */
+  molecule::BoundingBoxInfo getBoundingBox() const;
+
+  /** Getter to contained atoms contained in \a ObservedValues.
+   *
+   * \return molecule's contained atoms
+   */
+  atoms_t getPresentAtoms() const;
+
+  /** Counts how many ObservedValues got subjectKilled.
+   *
+   * This is used to give InstanceRemoved() signal only when each and every
+   * ObservedValue (and the instance itself) has been subjectKilled by the
+   * monitored Observable. Only then can we safely remove the instance.
+   *
+   */
+  void countsubjectKilled();
+
+  //!> counts how many ObservedValues have already been subjectKilled()
+  mutable size_t subjectKilledCount;
+
   //!> contains current version of the tesselation hull on request
   Cacheable<QGeometryData> TesselationHull;
-  //!> contains newest version of the bounding box on request
-  ObservedValue<molecule::BoundingBoxInfo> BoundingBox;
-  //!> contains the current live set of atoms for the molecule
-  ObservedValue<atoms_t> PresentAtoms;
-
+
+private:
   //!> contains the set of atoms displayed
   atoms_t DisplayedAtoms;

src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp

@@ -91 +91 @@
   }
   connect(this, SIGNAL(moleculePreparedInserted(const moleculeId_t)), this, SLOT(moleculeInserted(const moleculeId_t)));
-  connect(this, SIGNAL(moleculePreparedRemoved(const moleculeId_t)), this, SLOT(moleculeRemoved(const moleculeId_t)));
 
 //  connect(this, SIGNAL(updated()), this, SLOT(update()));
@@ -116 +115 @@
 //      moliter != molecules.end();
 //      moliter++) {
+//    boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);
 //    // check whether molecule already exists
 //    const moleculeId_t molid = (*moliter)->getId();
@@ -123 +123 @@
 //  }
 //
+//  boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);
 //  MoleculeNodeMap::iterator iter = MoleculesinSceneMap.begin();
 //  for (;iter != MoleculesinSceneMap.end();) {
@@ -182 +183 @@
 void GLWorldScene::atomInserted(const moleculeId_t _molid, const atomId_t _atomid)
 {
+  boost::recursive_mutex::scoped_lock lock(MoleculeMissedStateMap_mutex);
+
   LOG(3, "INFO: GLWorldScene: Received signal atomInserted for atom "+toString(_atomid)+".");
-
-  boost::recursive_mutex::scoped_lock lock(MoleculeMissedStateMap_mutex);
 
   // check of molecule is already present
@@ -268 +269 @@
 
   // add new object
+  LOG(1, "DEBUG: Adding GLMoleculeObject_molecule to id " << _id);
   GLMoleculeObject_molecule *molObject =
       new GLMoleculeObject_molecule(GLMoleculeObject::meshEmpty, this, _id);
@@ -344 +346 @@
   connect (molObject, SIGNAL(hoverChanged(const atomId_t)), this, SIGNAL(hoverChanged(const atomId_t)));
   connect (molObject, SIGNAL(hoverChanged(const moleculeId_t, int)), this, SIGNAL(hoverChanged(const moleculeId_t, int)));
-  connect (molObject, SIGNAL(indexChanged(GLMoleculeObject_molecule *, const moleculeId_t, const moleculeId_t)), this, SLOT(changeMoleculeId(GLMoleculeObject_molecule *, const moleculeId_t, const moleculeId_t)));
+  connect (molObject, SIGNAL(hoverChanged(const moleculeId_t, int)), this, SIGNAL(hoverChanged(const moleculeId_t, int)));
+  connect (molObject, SIGNAL(InstanceRemoved(const moleculeId_t)), this, SLOT(moleculeRemoved(const moleculeId_t)));
 
   emit changed();
@@ -350 +353 @@
 }
 
-/** Prepares removing a molecule from the scene.
- *
- * \sa moleculePrepareInserted()
+/** Removes a molecule from the scene.
+ *
+ * * \sa moleculePrepareRemoved()
  *
  * @param _id id of molecule to remove
  */
-void GLWorldScene::moleculePrepareRemoved(const moleculeId_t _id)
+void GLWorldScene::moleculeRemoved(const moleculeId_t _id)
 {
   LOG(3, "INFO: GLWorldScene: Received signal moleculePrepareRemoved for molecule "+toString(_id)+".");
@@ -363 +366 @@
 
   MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_id);
-  if ( iter == MoleculesinSceneMap.end())
+  if ( iter == MoleculesinSceneMap.end()) {
     RemovalMolecules.insert(_id);
-
-  emit moleculePreparedRemoved(_id);
-}
-
-/** Removes a molecule from the scene.
- *
- * * \sa moleculePrepareRemoved()
- *
- * @param _id id of molecule to remove
- */
-void GLWorldScene::moleculeRemoved(const moleculeId_t _id)
-{
-  boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);
-
-  MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_id);
-  GLMoleculeObject_molecule *molObject = iter->second;
-  molObject->disconnect();
-  MoleculesinSceneMap.erase(iter);
-  delete molObject;
+  } else {
+    LOG(1, "DEBUG: Removing GLMoleculeObject_molecule to id " << _id);
+    GLMoleculeObject_molecule *molObject = iter->second;
+    molObject->disconnect();
+    MoleculesinSceneMap.erase(iter);
+    delete molObject;
+  }
 
   // remove any possible state changes left
@@ -397 +388 @@
 void GLWorldScene::moleculesVisibilityChanged(const moleculeId_t _id, bool _visible)
 {
+  boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);
   MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_id);
   ASSERT( iter != MoleculesinSceneMap.end(),
@@ -506 +498 @@
 
   {
+    boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);
     // Remove from map.
     MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(oldId);
@@ -525 +518 @@
 
   {
+    boost::recursive_mutex::scoped_lock lock(MoleculeMissedStateMap_mutex);
     // Remove and re-insert from map if present.
     MoleculeMissedStateMap_t::iterator iter = MoleculeMissedStateMap.find(oldId);
@@ -537 +531 @@
 void GLWorldScene::AtomSelected(const moleculeId_t _molid, const atomId_t _id)
 {
+  boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);
   MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_molid);
   if (iter != MoleculesinSceneMap.end())
@@ -550 +545 @@
 void GLWorldScene::AtomUnselected(const moleculeId_t _molid, const atomId_t _id)
 {
+  boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);
   MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_molid);
   if (iter != MoleculesinSceneMap.end())
@@ -563 +559 @@
 void GLWorldScene::MoleculeSelected(const moleculeId_t _molid)
 {
-  MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_molid);
+  boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);
+MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_molid);
   if (iter != MoleculesinSceneMap.end())
     QMetaObject::invokeMethod(iter->second,        // pointer to a QObject
@@ -575 +572 @@
 void GLWorldScene::MoleculeUnselected(const moleculeId_t _molid)
 {
+  boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);
   MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_molid);
   if (iter != MoleculesinSceneMap.end())

src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp

@@ -83 +83 @@
   void hoverChanged(const moleculeId_t, int);
   void moleculePreparedInserted(const moleculeId_t _id);
-  void moleculePreparedRemoved(const moleculeId_t _id);
 
 private slots:
   void atomClicked(atomId_t no);
   void moleculeClicked(moleculeId_t no);
-  void moleculePrepareRemoved(const moleculeId_t _id);
   void moleculePrepareInserted(const moleculeId_t _id);
   void moleculeRemoved(const moleculeId_t _id);

src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp

@@ -93 +93 @@
   connect(this, SIGNAL(atomInserted(const moleculeId_t, const atomId_t)), worldscene, SLOT(atomInserted(const moleculeId_t, const atomId_t)), Qt::DirectConnection);
   connect(this, SIGNAL(moleculeInserted(const moleculeId_t)), worldscene, SLOT(moleculePrepareInserted(const moleculeId_t)), Qt::DirectConnection);
-  connect(this, SIGNAL(moleculeRemoved(const moleculeId_t)), worldscene, SLOT(moleculePrepareRemoved(const moleculeId_t)), Qt::DirectConnection);
   //connect(this, SIGNAL(changed()), this, SLOT(updateGL()));
   connect(this, SIGNAL(changed()), this, SLOT(sceneChangeSignalled()));
@@ -370 +369 @@
 
   if (mol != NULL) {
-
-    // sign off
-    signOffFromMolecule(mol);
+    ObservedMolecules.erase(mol);
+//
+//    // sign off
+//    signOffFromMolecule(mol);
 
     // emit removed signal