Changes in / [2f429e:d26fb7]

Files:

• src/Actions/AtomAction/AddAction.cpp (modified) (3 diffs)
• src/Actions/AtomAction/AddAction.def (modified) (1 diff)
• src/Atom/atom.cpp (modified) (1 diff)
• src/Graph/BondGraph.hpp (modified) (2 diffs)
• src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) (4 diffs)
• src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) (4 diffs)
• src/World.cpp (modified) (1 diff)
• src/molecule.cpp (modified) (11 diffs)
• src/molecule.hpp (modified) (4 diffs)
• tests/regression/Atoms/Add/post/test.pdb (modified) (1 diff)

src/Actions/AtomAction/AddAction.cpp

@@ -55 +55 @@
 #include "Action_impl_pre.hpp"
 /** =========== define the function ====================== */
+
+atom * getNewAtom(const AtomAddAction::AtomAddParameters &_params)
+{
+  atom * first = World::getInstance().createAtom();
+  first->setType(_params.elemental.get());
+  first->setPosition(_params.position.get());
+
+  return first;
+}
+
+std::vector<atomId_t> createAtoms(
+    const AtomAddAction::AtomAddParameters &_params,
+    std::vector<molecule *> &_molecules)
+{
+  std::vector<atomId_t> ids;
+  if (!_molecules.empty()) {
+    if (_molecules.size() == 1) {
+        atom *first = getNewAtom(_params);
+        molecule *mol = *_molecules.begin();
+        LOG(1, "Adding new atom with element " << first->getType()->getName()
+            << " at " << (first->getPosition()) << " to selected molecule "
+            << mol->getName()+".");
+        mol->AddAtom(first);
+      ids.push_back(first->getId());
+    }
+  } else {
+    atom *first = getNewAtom(_params);
+    molecule *mol = World::getInstance().createMolecule();
+    mol->setName("none");
+    mol->AddAtom(first);
+    LOG(1, "Adding new atom with element " << first->getType()->getName()
+        << " at " << (first->getPosition()) << " to new molecule.");
+    ids.push_back(first->getId());
+  }
+
+  return ids;
+}
+
 ActionState::ptr AtomAddAction::performCall() {
   // execute action
-  atom * first = World::getInstance().createAtom();
-  first->setType(params.elemental.get());
-  first->setPosition(params.position.get());
-  LOG(1, "Adding new atom with element " << first->getType()->getName() << " at " << (first->getPosition()) << ".");
-  // TODO: remove when all of World's atoms are stored.
-  std::vector<molecule *> molecules = World::getInstance().getAllMolecules();
-  if (!molecules.empty()) {
-    std::vector<molecule *>::iterator iter = molecules.begin();
-    (*iter)->AddAtom(first);
-  }
-  return ActionState::ptr(new AtomAddState(first->getId(), params));
+  std::vector<molecule *> molecules = World::getInstance().getSelectedMolecules();
+  std::vector<atomId_t> ids = createAtoms(params, molecules);
+
+  if (molecules.size() > 1)
+     return Action::failure;
+  else
+    return ActionState::ptr(new AtomAddState(ids, params));
 }
 
@@ -73 +107 @@
   AtomAddState *state = assert_cast<AtomAddState*>(_state.get());
 
-  LOG(1, "Removing atom with id " << state->id << ".");
-  World::getInstance().destroyAtom(state->id);
+  for (std::vector<atomId_t>::const_iterator iter = state->ids.begin();
+      iter != state->ids.end(); ++iter) {
+    LOG(1, "Removing atom with id " << *iter << ".");
+    World::getInstance().destroyAtom(*iter);
+  }
 
   return ActionState::ptr(_state);
@@ -82 +119 @@
   AtomAddState *state = assert_cast<AtomAddState*>(_state.get());
 
-  atom * first = World::getInstance().createAtom();
-  first->setType(state->params.elemental.get());
-  first->setPosition(state->params.position.get());
-  LOG(1, "Re-adding new atom with element " << state->params.elemental.get()->getName() << " at " << state->params.position.get() << ".");
-  // TODO: remove when all of World's atoms are stored.
-  std::vector<molecule *> molecules = World::getInstance().getAllMolecules();
-  if (!molecules.empty()) {
-    std::vector<molecule *>::iterator iter = molecules.begin();
-    (*iter)->AddAtom(first);
+  std::vector<molecule *> molecules = World::getInstance().getSelectedMolecules();
+  std::vector<atomId_t> newids = createAtoms(params, molecules);
+
+  if (newids.size() != state->ids.size()) {
+    STATUS("Could not recreate all atoms after undo.");
+    for (std::vector<atomId_t>::const_iterator iter = newids.begin(); iter != newids.end();++iter)
+      World::getInstance().destroyAtom(*iter);
+    return Action::failure;
   }
-  if (first->getId() != state->id)
-    if (!first->changeId(state->id)) {
-      STATUS("Could not change atom id "+toString(first->getId())+"->"+toString(state->id)+".");
-      return Action::failure;
-    }
 
-  return ActionState::ptr(_state);
+  std::vector<atomId_t>::const_iterator newiter = newids.begin();
+  std::vector<atomId_t>::const_iterator olditer = state->ids.begin();
+  bool status=true;
+  for (; newiter != newids.end(); ++newiter, ++olditer) {
+    atom * first = World::getInstance().getAtom(AtomById(*newiter));
+    ASSERT( first != NULL,
+        "AtomAddAction::performRedo() - re-created atom not present?");
+    if (first->getId() != *olditer)
+      if (!first->changeId(*olditer)) {
+        STATUS("Could not change atom id "+toString(first->getId())+"->"+toString(*olditer)+".");
+        // remove all created atoms
+        for (std::vector<atomId_t>::const_iterator iter = state->ids.begin(); iter != olditer;++iter)
+          World::getInstance().destroyAtom(*iter);
+        olditer = state->ids.end();
+        for (std::vector<atomId_t>::const_iterator iter = newiter; iter != newids.end();++iter)
+          World::getInstance().destroyAtom(*iter);
+        status = false;
+        break;
+      }
+  }
+  ASSERT( olditer == state->ids.end(),
+      "AtomAddAction::performRedo() - after all unequal amount of ids in new and old?");
+
+  if (!status) {
+    return Action::failure;
+  } else
+    return ActionState::ptr(_state);
 }
 

src/Actions/AtomAction/AddAction.def

@@ -27 +27 @@
 (BoxVectorValidator())
 
-#define statetypes (const atomId_t)
-#define statereferences (id)
+#define statetypes (std::vector<atomId_t>)
+#define statereferences (ids)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS

src/Atom/atom.cpp

@@ -264 +264 @@
   // first we move ourselves in the world
   // the world lets us know if that succeeded
+  atomId_t oldid = id;
   if(world->changeAtomId(id,newId,this)){
     OBSERVE;
     id = newId;
+    if (mol != NULL)
+      mol->changeAtomId(oldid, newId);
     NOTIFY(IndexChanged);
     return true;

src/Graph/BondGraph.hpp

@@ -221 +221 @@
               neighboriter != ListOfNeighbors.end();
               ++neighboriter) {
-            if ((*neighboriter) > Walker) {  // just to not add bonds from both sides
-              const atom * const OtherWalker = dynamic_cast<const atom *>(*neighboriter);
-              ASSERT(OtherWalker != NULL,
-                  "BondGraph::CreateAdjacency() - TesselPoint "
-                  +(*neighboriter)->getName()+" that was not an atom retrieved from LinkedList");
+            const atom * const OtherWalker = dynamic_cast<const atom *>(*neighboriter);
+            ASSERT(OtherWalker != NULL,
+                "BondGraph::CreateAdjacency() - TesselPoint "
+                +(*neighboriter)->getName()+" that was not an atom retrieved from LinkedList");
+            if (OtherWalker->getId() > Walker->getId()) {  // just to not add bonds from both sides
               LOG(4, "INFO: Current other atom is " << *OtherWalker << ".");
 
@@ -245 +245 @@
               }
             } else {
-              LOG(5, "REJECT: Not Adding: Wrong order.");
+              LOG(4, "REJECT: Not Adding: Wrong order.");
             }
           }

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

@@ -85 +85 @@
 const Observable::channels_t GLMoleculeObject_molecule::AtomsChannels(getAtomsChannels());
 const Observable::channels_t GLMoleculeObject_molecule::HullChannels(getAllAtomicChangesChannels());
-const Observable::channels_t GLMoleculeObject_molecule::BoundingBoxChannels(getAllAtomicChangesChannels());
+const Observable::channels_t GLMoleculeObject_molecule::BoundingBoxChannels(1, molecule::BoundingBoxChanged);
 const Observable::channels_t GLMoleculeObject_molecule::IndexChannels(1, molecule::IndexChanged);
 const Observable::channels_t GLMoleculeObject_molecule::NameChannels(1, molecule::MoleculeNameChanged);
@@ -403 +403 @@
 }
 
-GLMoleculeObject_molecule::BoundingBoxInfo GLMoleculeObject_molecule::initBoundingBox() const
-{
-  BoundingBoxInfo info;
+molecule::BoundingBoxInfo GLMoleculeObject_molecule::initBoundingBox() const
+{
+  molecule::BoundingBoxInfo info;
   info.position = zeroVec;
   info.radius = 0.;
@@ -411 +411 @@
 }
 
-GLMoleculeObject_molecule::BoundingBoxInfo GLMoleculeObject_molecule::updateBoundingBox() const
-{
-  BoundingBoxInfo info = BoundingBox.get();
+molecule::BoundingBoxInfo GLMoleculeObject_molecule::updateBoundingBox() const
+{
+  molecule::BoundingBoxInfo info = BoundingBox.get();
   const molecule * const _molecule = getMolecule(MolIndex.get());
   if (_molecule != NULL) {
@@ -472 +472 @@
 void GLMoleculeObject_molecule::resetBoundingBox()
 {
-  BoundingBoxInfo info = BoundingBox.get();
+  molecule::BoundingBoxInfo info = BoundingBox.get();
   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

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

@@ -24 +24 @@
 #include "GLMoleculeObject_bond.hpp"
 
+#include "molecule.hpp"
+
 class atom;
 class bond;
 class GLMoleculeObject_atom;
 class GLWorldScene;
-class molecule;
 
 class GLMoleculeObject_molecule : public GLMoleculeObject, public Observer
@@ -109 +110 @@
   typedef std::set<atomId_t> atoms_t;
 
-  /** Structure for the required information on the bounding box.
-   *
-   */
-  struct BoundingBoxInfo {
-    //!> position of center
-    Vector position;
-    //!> radius of sphere
-    double radius;
-  };
-
-  /** Structure for the required information on the tesselation hull.
-   *
-   */
-  struct TesselationHullInfo {
-  };
-
-  BoundingBoxInfo initBoundingBox() const;
+  molecule::BoundingBoxInfo initBoundingBox() const;
 
   QGeometryData updateTesselationHull() const;
-  BoundingBoxInfo updateBoundingBox() const;
+  molecule::BoundingBoxInfo updateBoundingBox() const;
   atoms_t updateAtoms();
   moleculeId_t updateIndex() const;
@@ -153 +138 @@
   boost::function<std::string ()> MolNameUpdater;
   boost::function<QGeometryData ()> TesselationHullUpdater;
-  boost::function<BoundingBoxInfo ()> BoundingBoxUpdater;
+  boost::function<molecule::BoundingBoxInfo ()> BoundingBoxUpdater;
   boost::function<atoms_t ()> PresentAtomsUpdater;
 
@@ -163 +148 @@
   Cacheable<QGeometryData> TesselationHull;
   //!> contains newest version of the bounding box on request
-  ObservedValue<BoundingBoxInfo> BoundingBox;
+  ObservedValue<molecule::BoundingBoxInfo> BoundingBox;
   //!> contains the current live set of atoms for the molecule
   ObservedValue<atoms_t> PresentAtoms;

src/World.cpp

@@ -396 +396 @@
   if (isAtomSelected(id))
     selectedAtoms.erase(id);
+  DeleteAtom(atom);
   atoms.erase(id);
-  DeleteAtom(atom);
   atomIdPool.releaseId(id);
   // remove molecule if empty

src/molecule.cpp

@@ -36 +36 @@
 
 #include <algorithm>
+#include <boost/assign.hpp>
 #include <boost/bind.hpp>
 #include <boost/foreach.hpp>
@@ -50 +51 @@
 #include "CodePatterns/enumeration.hpp"
 #include "CodePatterns/Log.hpp"
+#include "CodePatterns/Observer/Observable.hpp"
 #include "CodePatterns/Observer/Notification.hpp"
 #include "config.hpp"
@@ -67 +69 @@
 #include "WorldTime.hpp"
 
+using namespace boost::assign;
+
+// static entities
+static Observable::channels_t getBoundingBoxChannels()
+{
+  Observable::channels_t channels;
+  channels += molecule::AtomInserted, molecule::AtomRemoved, molecule::AtomMoved;
+  return channels;
+}
 
 /************************************* Functions for class molecule *********************************/
@@ -83 +94 @@
   BondCount(this,boost::bind(&molecule::doCountBonds,this),"BondCount"),
   atomIdPool(1, 20, 100),
+  BoundingBoxSweepingAxis(std::vector<AtomDistanceMap_t>(NDIM)),
   _lastchangedatomid(-1),
   last_atom(0)
@@ -92 +104 @@
     OurChannel->addChannel(type);
 
+  // cannot initialize in initializer body as then channels have not been setup yet
+  BoundingBox.reset(
+      new Cacheable<BoundingBoxInfo>(
+          this, boost::bind(&molecule::updateBoundingBox, boost::cref(this)), "molecule_BoundingBox", getBoundingBoxChannels()));
+
   strcpy(name,World::getInstance().getDefaultName().c_str());
-};
+}
 
 molecule *NewMolecule(){
@@ -170 +187 @@
 }
 
+bool molecule::changeAtomId(int oldId, int newId)
+{
+  OBSERVE;
+  if ((!atomIds.contains( oldId )) || (atomIds.contains( newId )))
+    return false;
+  atomIds.erase( oldId );
+  atomIds.insert( newId );
+  // also update BoundingBoxSweepingAxis
+  for (int i=0;i<NDIM;++i) {
+    AtomDistanceMap_t::left_iterator iter = BoundingBoxSweepingAxis[i].left.find(oldId);
+    ASSERT(iter != BoundingBoxSweepingAxis[i].left.end(),
+        "molecule::changeAtomId() - could not find atom "+toString(oldId)
+        +" in BoundingBoxSweepingAxis.");
+    const double component = iter->second;
+    BoundingBoxSweepingAxis[i].left.erase(iter);
+    BoundingBoxSweepingAxis[i].left.insert( std::make_pair(newId, component) );
+  }
+  return true;
+}
+
 bool molecule::changeId(moleculeId_t newId){
   // first we move ourselves in the world
@@ -227 +264 @@
   atomIds.erase( _atom->getId() );
   {
+    BoundingBoxInfo oldinfo = updateBoundingBox();
+    for (int i=0;i<NDIM;++i)
+      BoundingBoxSweepingAxis[i].left.erase( _atom->getId() );
+    BoundingBoxInfo newinfo = updateBoundingBox();
+    if (oldinfo != newinfo)
+      NOTIFY(BoundingBoxChanged);
+  }
+  {
     NOTIFY(AtomNrChanged);
     atomIdPool.releaseId(_atom->getNr());
@@ -240 +285 @@
 molecule::const_iterator molecule::erase( atom * key )
 {
-  OBSERVE;
-  {
-    _lastchangedatomid = key->getId();
-    NOTIFY(AtomRemoved);
-  }
   const_iterator iter = const_cast<const molecule &>(*this).find(key);
-  if (iter != const_cast<const molecule &>(*this).end()){
-    ++iter;
-    atomIds.erase( key->getId() );
-    {
-      NOTIFY(AtomNrChanged);
-      atomIdPool.releaseId(key->getNr());
-      LocalToGlobalId.erase(key->getNr());
-      key->setNr(-1);
-    }
-    NOTIFY(FormulaChanged);
-    formula-=key->getType();
-    key->removeFromMolecule();
-  }
-  return iter;
+  if (iter != const_cast<const molecule &>(*this).end())
+    return erase(iter);
+  else
+    return iter;
 }
 
@@ -269 +299 @@
   std::pair<iterator,bool> res = atomIds.insert(key->getId());
   if (res.second) { // push atom if went well
+    {
+      BoundingBoxInfo oldinfo = updateBoundingBox();
+      for (int i=0;i<NDIM;++i)
+        BoundingBoxSweepingAxis[i].left.insert( std::make_pair(key->getId(), key->getPosition()[i]));
+      BoundingBoxInfo newinfo = updateBoundingBox();
+      if (oldinfo != newinfo)
+        NOTIFY(BoundingBoxChanged);
+    }
     NOTIFY(AtomNrChanged);
     key->setNr(atomIdPool.getNextId());
@@ -1038 +1076 @@
 }
 
+molecule::BoundingBoxInfo molecule::updateBoundingBox() const
+{
+  BoundingBoxInfo info;
+  Vector min = zeroVec;
+  Vector max = zeroVec;
+  for (int i=0;i<NDIM;++i) {
+    if (!BoundingBoxSweepingAxis[i].right.empty()) {
+      min[i] = BoundingBoxSweepingAxis[i].right.begin()->first;
+      max[i] = BoundingBoxSweepingAxis[i].right.rbegin()->first;
+    }
+  }
+  info.radius = (.5*(max-min)).Norm();
+  info.position = .5*(max+min);
+  return info;
+}
+
+molecule::BoundingBoxInfo molecule::getBoundingBox() const
+{
+  return **BoundingBox;
+}
+
 void molecule::update(Observable *publisher)
 {
@@ -1057 +1116 @@
         // emit others about one of our atoms moved
         _lastchangedatomid = _atom->getId();
+        // update entry in map
+        BoundingBoxInfo oldinfo = updateBoundingBox();
+        for (int i=0;i<NDIM;++i) {
+          AtomDistanceMap_t::left_iterator iter = BoundingBoxSweepingAxis[i].left.find(_atom->getId());
+          ASSERT(iter != BoundingBoxSweepingAxis[i].left.end(),
+              "molecule::recieveNotification() - could not find atom "+toString(_atom->getId())
+              +" in BoundingBoxSweepingAxis.");
+          BoundingBoxSweepingAxis[i].left.erase(iter);
+          BoundingBoxSweepingAxis[i].left.insert(
+              std::make_pair(_atom->getId(), _atom->getPosition()[i]) );
+        }
+        BoundingBoxInfo newinfo = updateBoundingBox();
         OBSERVE;
         NOTIFY(AtomMoved);
+        if (oldinfo != newinfo)
+          NOTIFY(BoundingBoxChanged);
         break;
       }

src/molecule.hpp

@@ -22 +22 @@
 
 #include <string>
+
+#include <boost/bimap/bimap.hpp>
+#include <boost/bimap/unordered_set_of.hpp>
+#include <boost/bimap/multiset_of.hpp>
+#include <boost/optional.hpp>
+#include <boost/shared_ptr.hpp>
 
 #include "AtomIdSet.hpp"
@@ -115 +121 @@
     MoleculeNameChanged,
     IndexChanged,
+    BoundingBoxChanged,
     AboutToBeRemoved,
     NotificationType_MAX
@@ -238 +245 @@
   bool changeAtomNr(int oldNr, int newNr, atom* target=0);
 
+  friend bool atom::changeId(atomId_t newId);
+  /**
+   * used when changing an ParticleInfo::Id.
+   * Note that this number is global (and the molecule uses it to know which atoms belong to it)
+   *
+   * @param oldId old Id
+   * @param newId new Id to set
+   * @return indicates wether the change could be done or not.
+   */
+  bool changeAtomId(int oldId, int newId);
+
   /** Updates the internal lookup fro local to global indices.
    *
@@ -260 +278 @@
 
 public:
+
+  /** Structure for the required information on the bounding box.
+   *
+   */
+  struct BoundingBoxInfo {
+    //!> position of center
+    Vector position;
+    //!> radius of sphere
+    double radius;
+
+    /** Equivalence operator for bounding box.
+     *
+     * \return true - both bounding boxes have same position and radius
+     */
+    bool operator==(const BoundingBoxInfo &_other) const
+    {  return (radius == _other.radius) && (position == _other.position); }
+
+    /** Inequivalence operator for bounding box.
+     *
+     * \return true - bounding boxes have either different positions or different radii or both
+     */
+    bool operator!=(const BoundingBoxInfo &_other) const
+    { return !(*this == _other); }
+  };
+
+private:
+
+  /** Returns the current bounding box.
+   *
+   * \return Shape with center and extension of box
+   */
+  BoundingBoxInfo updateBoundingBox() const;
+
+  // stuff for keeping bounding box up-to-date efficiently
+
+  //!> Cacheable for the bounding box, ptr such that
+  boost::shared_ptr< Cacheable<BoundingBoxInfo> > BoundingBox;
+  /** Bimap storing atomic ids and the component per axis.
+   *
+   * We need a bimap in order to have the components sorted and be able to
+   * access max and min values in linear time and also access the ids in
+   * constant time in order to update the map, when atoms move, are inserted,
+   * or removed.
+   */
+  typedef boost::bimaps::bimap<
+          boost::bimaps::unordered_set_of< atomId_t >,
+          boost::bimaps::multiset_of< double, std::greater<double> >
+      > AtomDistanceMap_t;
+  std::vector<AtomDistanceMap_t> BoundingBoxSweepingAxis;
+
+public:
+
+  /** Returns the current bounding box of this molecule.
+   *
+   * \return bounding box info with center and radius
+   */
+  BoundingBoxInfo getBoundingBox() const;
 
   /** Function to create a bounding spherical shape for the currently associated atoms.

tests/regression/Atoms/Add/post/test.pdb

@@ -1 +1 @@
 REMARK created by molecuilder on Wed Feb  2 18:06:07 2011
-ATOM      1 H01 0-   00         10.000  10.000  10.000  0.00  0.00           H 0
+ATOM      1 H01 0non 01         10.000  10.000  10.000  0.00  0.00           H 0
 END