Changeset c30959

Timestamp:

Apr 23, 2021, 8:51:43 PM (5 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.0, stable

Children:

f01bb3

Parents:

e70818

git-author:

Frederik Heber <frederik.heber@…> (11/17/20 22:25:47)

git-committer:

Frederik Heber <frederik.heber@…> (04/23/21 20:51:43)

Message:

BondAddAction also adds to molecule.

• NOTE: This basically does nothing as new atoms (AddAtom action) always get a dummy molecule. However, removing them from the dummy molecule and readding one is quite complicated.
• if we add bonds between new atoms (without a molecule set) to and atoms belonging all to the same molecule, then we automatically add the new atoms to this molecule as well. This saves the need for any GraphUpdateMolecules() call afterwards.
• also implemented undo and redo for this.

Location:

src/Actions/BondAction

Files:

• BondAddAction.cpp (modified) (6 diffs)
• BondAddAction.def (modified) (2 diffs)

src/Actions/BondAction/BondAddAction.cpp

@@ -41 +41 @@
 #include "CodePatterns/Verbose.hpp"
 #include "Descriptors/AtomIdDescriptor.hpp"
+#include "molecule.hpp"
 #include "World.hpp"
 #include "WorldTime.hpp"
@@ -63 +64 @@
   }
 
+  // check if we are adding new atoms to a molecule
+  molecules_t molecules;
+  const molecule *add_to_mol_const = NULL;
+  molecules.reserve(world.countSelectedAtoms());
+  for (World::AtomSelectionConstIterator firstiter = world.beginAtomSelection();
+      firstiter != world.endAtomSelection(); ++firstiter) {
+    const molecule * const current_mol = firstiter->second->getMolecule();
+    molecules.push_back(current_mol);
+    if (current_mol != NULL) {
+      if (add_to_mol_const == NULL)
+        add_to_mol_const = current_mol;
+      else if (add_to_mol_const != current_mol) {
+        // we encountered a second molecule, don't set the molecules
+        molecules.clear();
+        add_to_mol_const = NULL;
+        break;
+      }
+    }
+  }
+
   bondPairIds_t bondPairIds;
   for (World::AtomSelectionConstIterator firstiter = world.beginAtomSelection();
@@ -81 +102 @@
 
   // create undo
-  BondAddState *UndoState = new BondAddState(bondPairIds, params);
+  molecule *add_to_mol = NULL;
+  if (add_to_mol_const != NULL) {
+    add_to_mol = world.getMolecule(MoleculeById(add_to_mol_const->getId()));
+    ASSERT( add_to_mol != NULL,
+        "BondAddAction::performCall() - could not obtain molecule from World.");
+  }
+  BondAddState *UndoState = new BondAddState(bondPairIds, molecules, add_to_mol, params);
 
   // execute action
   for (bondPairIds_t::const_iterator iter = bondPairIds.begin();
       iter != bondPairIds.end(); ++iter) {
-    atom *firstatom = world.getAtom(AtomById(iter->first));
-    atom *secondatom = world.getAtom(AtomById(iter->second));
+    atom * const firstatom = world.getAtom(AtomById(iter->first));
+    atom * const secondatom = world.getAtom(AtomById(iter->second));
     ASSERT((firstatom != NULL) && (secondatom != NULL),
         "BondAddAction::performCall() - at least one of the ids "
@@ -97 +124 @@
       +toString(*firstatom)+" and "+toString(*secondatom)+" failed.");
   }
+  if (add_to_mol != NULL)
+    for (World::AtomSelectionIterator firstiter = world.beginAtomSelection();
+        firstiter != world.endAtomSelection(); ++firstiter) {
+      if (firstiter->second->getMolecule() != add_to_mol)
+        add_to_mol->AddAtom(firstiter->second);
+    }
 
   return ActionState::ptr(UndoState);
@@ -120 +153 @@
     }
   }
+  if (state->add_to_mol != NULL) {
+    molecules_t::const_iterator mol_iter = state->molecules.begin();
+    for (World::AtomSelectionIterator firstiter = world.beginAtomSelection();
+        firstiter != world.endAtomSelection(); ++firstiter) {
+      const molecule * const current_mol = *mol_iter++;
+      atom * const Walker = firstiter->second;
+      if (current_mol != Walker->getMolecule()) {
+        if (Walker->getMolecule() != NULL)
+          Walker->removeFromMolecule();
+        if (current_mol != NULL) {
+          molecule *add_to_mol = world.getMolecule(MoleculeById(current_mol->getId()));
+          add_to_mol->AddAtom(Walker);
+        }
+      }
+    }
+    ASSERT(mol_iter == state->molecules.end(),
+        "BondAddAction::performUndo() - number of molecule ptrs not coinciding with number of selected atoms.");
+  }
 
   return ActionState::ptr(_state);
@@ -143 +194 @@
     }
   }
+  if (state->add_to_mol != NULL)
+    for (World::AtomSelectionIterator firstiter = world.beginAtomSelection();
+        firstiter != world.endAtomSelection(); ++firstiter) {
+      if (firstiter->second->getMolecule() != state->add_to_mol)
+        state->add_to_mol->AddAtom(firstiter->second);
+    }
 
   return ActionState::ptr(_state);

src/Actions/BondAction/BondAddAction.def

@@ -12 +12 @@
 
 typedef std::vector<std::pair<atomId_t,atomId_t> > bondPairIds_t;
+typedef std::vector<const molecule*> molecules_t;
 
 #include "Parameters/Validators/RangeValidator.hpp"
@@ -27 +28 @@
 (RangeValidator<int>(1,10))
 
-#define statetypes (bondPairIds_t)
-#define statereferences (bondPairIds)
+#define statetypes (bondPairIds_t)(molecules_t)(molecule *)
+#define statereferences (bondPairIds)(molecules)(add_to_mol)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS