Changeset 25aa214

Timestamp:

Dec 19, 2025, 11:29:38 PM (9 days ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.1, stable

Children:

98ad30

Parents:

d2be22

git-author:

Frederik Heber <frederik.heber@…> (11/16/25 11:19:01)

git-committer:

Frederik Heber <frederik.heber@…> (12/19/25 23:29:38)

Message:

FIX: fragmentation hydrogens do not trigger AtomInserted.

• we had already switched off position and element changes. However, the fragmentation hydrogens could still be briefly seen on creation because the AtomInserted notification is still triggered. The World::createAtom allows now to suppress the notifcation. The switch options are put into an enum to make them very verbose in the code. This should really only be used by the HydrogenPool.

Location:

src

Files:

• Filling/unittests/IsVoidNode_FillPredicateUnitTest.cpp (modified) (1 diff)
• Filling/unittests/Ops_FillPredicateUnitTest.cpp (modified) (1 diff)
• Fragmentation/Exporters/HydrogenPool.cpp (modified) (1 diff)
• Fragmentation/Exporters/unittests/SaturationDistanceMaximizerUnitTest.cpp (modified) (1 diff)
• World.cpp (modified) (2 diffs)
• World.hpp (modified) (1 diff)
• unittests/AtomIdSetUnitTest.cpp (modified) (1 diff)
• unittests/MoleculeUnitTest.cpp (modified) (1 diff)

src/Filling/unittests/IsVoidNode_FillPredicateUnitTest.cpp

@@ -80 +80 @@
   // create some atoms as "neighbours"
   atoms.resize((size_t)5, NULL);
-  std::generate_n(atoms.begin(), (size_t)5, boost::bind(&World::createAtom, World::getPointer()) );
+  std::generate_n(atoms.begin(), (size_t)5, boost::bind(
+    static_cast<atom* (World::*)(World::CreateAtomNotificationType)>(&World::createAtom), 
+    World::getPointer(), 
+    World::CreateAtomNotificationType::NOTIFY_ON_CREATE_ATOM) 
+  );
 
   // position them

src/Filling/unittests/Ops_FillPredicateUnitTest.cpp

@@ -79 +79 @@
   // create some atoms as "neighbours"
   atoms.resize((size_t)5, NULL);
-  std::generate_n(atoms.begin(), (size_t)5, boost::bind(&World::createAtom, World::getPointer()) );
+  std::generate_n(atoms.begin(), (size_t)5, boost::bind(
+    static_cast<atom* (World::*)(World::CreateAtomNotificationType)>(&World::createAtom), 
+    World::getPointer(), 
+    World::CreateAtomNotificationType::NOTIFY_ON_CREATE_ATOM)  );
 
   // position them

src/Fragmentation/Exporters/HydrogenPool.cpp

@@ -60 +60 @@
 {
   // get new hydrogen from world, but remove its observers
-  atom * const Walker = World::getInstance().createAtom();
+  atom * const Walker = World::getInstance().createAtom(World::CreateAtomNotificationType::DO_NOT_NOTIFY);
   Walker->setType(HYDROGEN);  // set element
   Walker->setName(std::string("H_")+toString(HydrogenCount));

src/Fragmentation/Exporters/unittests/SaturationDistanceMaximizerUnitTest.cpp

@@ -87 +87 @@
   // prepare SaturatedBonds each with degree one
   atomVector.resize((size_t)MaxAtoms);
-  std::generate_n(atomVector.begin(), MaxAtoms,
-      boost::bind(&World::createAtom, boost::ref(World::getInstance())));
+  std::generate_n(atomVector.begin(), MaxAtoms, boost::bind(
+      static_cast<atom* (World::*)(World::CreateAtomNotificationType)>(&World::createAtom), 
+      World::getPointer(), 
+      World::CreateAtomNotificationType::NOTIFY_ON_CREATE_ATOM));
   std::list<bond*> bondVector;
   SaturationDistanceMaximizer::PositionContainers_t PositionContainers;

src/World.cpp

@@ -391 +391 @@
 }
 
-atom *World::createAtom(){
+atom *World::createAtom(const CreateAtomNotificationType _notify){
   OBSERVE;
   atomId_t id = atomIdPool.getNextId();
@@ -401 +401 @@
   _lastchangedatom = res;
   _lastchangedatomid = res->getId();
-  NOTIFY(AtomInserted);
+  if (_notify == NOTIFY_ON_CREATE_ATOM)
+    NOTIFY(AtomInserted);
   return res;
 }

src/World.hpp

@@ -337 +337 @@
   void destroyMolecule(moleculeId_t);
 
+  /** Enumeration of a notification boolean switch that makes it more readible.
+   */
+  enum CreateAtomNotificationType {
+    NOTIFY_ON_CREATE_ATOM,  //!< default
+    DO_NOT_NOTIFY           //!< this should only be used by the \a HydrogenPool for fragmentation hydrogens 
+  };
+
   /**
    * Create a new atom. This method should be used whenever any atom is needed. Assigns a unique ID and stores
    * the atom in the World. If the atom is not destroyed it will automatically be destroyed when the world ends.
-   */
-  atom *createAtom();
+   *
+   * \param _notify - if do not notify, then the AtomInserted channel receives no update, used by \a HydrogenPool.
+   */
+  atom *createAtom(const CreateAtomNotificationType _notify = NOTIFY_ON_CREATE_ATOM);
 
   /**

src/unittests/AtomIdSetUnitTest.cpp

@@ -63 +63 @@
 
   atomVector.resize((size_t)MaxAtoms);
-  std::generate_n(atomVector.begin(), MaxAtoms,
-      boost::bind(&World::createAtom, boost::ref(World::getInstance())));
+  std::generate_n(atomVector.begin(), MaxAtoms, boost::bind(
+    static_cast<atom* (World::*)(World::CreateAtomNotificationType)>(&World::createAtom), 
+    World::getPointer(), 
+    World::CreateAtomNotificationType::NOTIFY_ON_CREATE_ATOM)
+  );
 }
 

src/unittests/MoleculeUnitTest.cpp

@@ -64 +64 @@
 
   atomVector.resize((size_t)MaxAtoms);
-  std::generate_n(atomVector.begin(), MaxAtoms,
-      boost::bind(&World::createAtom, boost::ref(World::getInstance())));
+  std::generate_n(atomVector.begin(), MaxAtoms, boost::bind(
+    static_cast<atom* (World::*)(World::CreateAtomNotificationType)>(&World::createAtom), 
+    World::getPointer(), 
+    World::CreateAtomNotificationType::NOTIFY_ON_CREATE_ATOM)
+  );
   std::for_each(atomVector.begin(), atomVector.end(),
       boost::bind(static_cast<void (AtomInfo::*)(int)>(&AtomInfo::setType), _1, (atomicNumber_t)1));