Changes in / [0ac85c3:7b38d3]


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Files:
2 added
81 deleted
67 edited

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  • doc/userguide/userguide.xml

    r0ac85c3 r7b38d3  
    629629                </programlisting>
    630630              </listitem>
    631 
    632               <listitem>
    633                 <para>Push/Pop the current selection to/from a stack to store
    634                 it momentarily and allow modifications in MakroActions.</para>
    635                 <programlisting>
    636                 ... --push-atom-selection
    637                 </programlisting>
    638                 <programlisting>
    639                 ... --pop-atom-selection
    640                 </programlisting>
    641               </listitem>
    642631            </itemizedlist>
    643632          </listitem>
    … …  
    720709                <programlisting>
    721710                ... --unselect-atoms-molecules
    722                 </programlisting>
    723               </listitem>
    724 
    725               <listitem>
    726                 <para>Push/Pop the current selection to/from a stack to store
    727                 it momentarily and allow modifications in MakroActions.</para>
    728                 <programlisting>
    729                 ... --push-molecule-selection
    730                 </programlisting>
    731                 <programlisting>
    732                 ... --pop-molecule-selection
    733711                </programlisting>
    734712              </listitem>
    … …  
    12691247            (without suffix) as its name.</para>
    12701248          </note>
    1271         </section>
    1272 
    1273         <section xml:id='molecule.remove-molecule'>
    1274           <title xml:id='molecule.remove-molecule.title'>Remove molecules
    1275           </title>
    1276 
    1277           <para>This removes one or multiple selected molecules.</para>
    1278 
    1279           <programlisting>... -remove-molecule</programlisting>
    1280 
    1281           <para>This essentially just removes all of the molecules' atoms
    1282           which in turn also causes the removal of the molecule.</para>
    1283         </section>
    1284 
    1285         <section xml:id='molecule.translate-molecules'>
    1286           <title xml:id='molecule.translate-molecules.title'>Translate molecules
    1287           </title>
    1288 
    1289           <para>This translates one or multiple selected molecules by a
    1290           specific offset..</para>
    1291 
    1292           <programlisting>... -translate-molecules</programlisting>
    1293 
    1294           <para>This essentially translates all of the molecules' atoms.</para>
    12951249        </section>
    12961250

  • src/Actions/Action.cpp

    r0ac85c3 r7b38d3  
    146146  endTimer();
    147147
    148   if (shouldUndo() && state != Action::failure) {
    149     if (canUndo()) {
     148  if(shouldUndo() && state != failure){
     149    if(canUndo()){
    150150      ActionQueue::getInstance().addElement(this,state);
    151151    }
    152 //    else{
    153 //      ActionQueue::getInstance().clear();
    154 //    }
     152    else{
     153      ActionQueue::getInstance().clear();
     154    }
    155155  }
    156156

  • src/Actions/ActionQueue.cpp

    r0ac85c3 r7b38d3  
    4444#include <boost/date_time/posix_time/posix_time.hpp>
    4545#include <boost/version.hpp>
    46 #include <iterator>
    4746#include <string>
    4847#include <sstream>
    … …  
    6261    AR(new ActionRegistry()),
    6362    history(new ActionHistory),
     63    CurrentAction(0),
    6464#ifndef HAVE_ACTION_THREAD
    6565    lastActionOk(true)
    6666#else
    67     CurrentAction(0),
    6867    lastActionOk(true),
    6968    run_thread(boost::bind(&ActionQueue::run, this)),
    … …  
    8382#ifdef HAVE_ACTION_THREAD
    8483  stop();
    85 
    86   clearTempQueue();
    8784#endif
    8885
    … …  
    114111    std::cerr << "Action " << *boost::get_error_info<ActionNameString>(e) << " has failed." << std::endl;
    115112    World::getInstance().setExitFlag(5);
    116     clearQueue(actionqueue.size()-1);
     113    clearQueue();
    117114    lastActionOk = false;
    118     std::cerr << "Remaining Actions cleared from queue." << std::endl;
     115    std::cerr << "ActionQueue cleared." << std::endl;
    119116  } catch (std::exception &e) {
    120117    pushStatus("FAIL: General exception caught, aborting.");
    121118    World::getInstance().setExitFlag(134);
    122     clearQueue(actionqueue.size()-1);
     119    clearQueue();
    123120    lastActionOk = false;
    124     std::cerr << "Remaining Actions cleared from queue." << std::endl;
     121    std::cerr << "ActionQueue cleared." << std::endl;
    125122  }
    126123  if (lastActionOk) {
    … …  
    130127  }
    131128#else
    132   setRunThreadIdle(CurrentAction == actionqueue.size());
     129  {
     130    boost::lock_guard<boost::mutex> lock(mtx_idle);
     131    run_thread_isIdle = (CurrentAction == actionqueue.size());
     132  }
    133133  mtx_queue.unlock();
    134134#endif
    … …  
    144144  mtx_queue.lock();
    145145  tempqueue.push_back( newaction );
    146   setRunThreadIdle( !((CurrentAction != actionqueue.size()) || !tempqueue.empty()) );
     146  {
     147    boost::lock_guard<boost::mutex> lock(mtx_idle);
     148    run_thread_isIdle = !((CurrentAction != actionqueue.size()) || !tempqueue.empty());
     149  }
    147150  mtx_queue.unlock();
    148151#endif
    … …  
    181184        pushStatus("FAIL: Action "+*boost::get_error_info<ActionNameString>(e)+" has failed.");
    182185        World::getInstance().setExitFlag(5);
    183         clearQueue(CurrentAction);
    184         clearTempQueue();
     186        clearQueue();
    185187        lastActionOk = false;
    186         std::cerr << "Remaining Actions cleared from queue." << std::endl;
     188        std::cerr << "ActionQueue cleared." << std::endl;
     189        CurrentAction = (size_t)-1;
    187190      } catch (std::exception &e) {
    188191        pushStatus("FAIL: General exception caught, aborting.");
    189192        World::getInstance().setExitFlag(134);
    190         clearQueue(CurrentAction);
    191         clearTempQueue();
    192         std::cerr << "Remaining Actions cleared from queue." << std::endl;
     193        clearQueue();
     194        std::cerr << "ActionQueue cleared." << std::endl;
     195        CurrentAction = (size_t)-1;
    193196      }
    194197      if (lastActionOk) {
    … …  
    196199        NOTIFY(ActionQueued);
    197200        _lastchangedaction = actionqueue[CurrentAction];
    198         mtx_queue.lock();
    199         CurrentAction++;
    200         mtx_queue.unlock();
    201201      }
    202202      // access actionqueue, hence using mutex
    203203      mtx_queue.lock();
     204      // step on to next action and check for end
     205      CurrentAction++;
    204206      // insert new actions (before [CurrentAction]) if they have been spawned
    205207      // we must have an extra vector for this, as we cannot change actionqueue
    … …  
    209211      mtx_queue.unlock();
    210212    }
    211     setRunThreadIdle( !((CurrentAction != actionqueue.size()) || !tempqueue.empty()) );
     213    {
     214      boost::lock_guard<boost::mutex> lock(mtx_idle);
     215      run_thread_isIdle = !((CurrentAction != actionqueue.size()) || !tempqueue.empty());
     216    }
    212217    cond_idle.notify_one();
    213218//    LOG(1, "DEBUG: End of ActionQueue's run() loop.");
    214219  } while (!Interrupted);
    215220}
     221#endif
    216222
    217223void ActionQueue::insertTempQueue()
    … …  
    225231}
    226232
     233#ifdef HAVE_ACTION_THREAD
    227234void ActionQueue::wait()
    228235{
    … …  
    309316}
    310317
    311 void ActionQueue::clearQueue(const size_t _fromAction)
    312 {
    313 #ifdef HAVE_ACTION_THREAD
    314   mtx_queue.lock();
    315 #endif
    316   LOG(1, "Removing all Actions from position " << _fromAction << " onward.");
    317   // free all actions still to be called contained in actionqueue
    318   ActionQueue_t::iterator inititer = actionqueue.begin();
    319   std::advance(inititer, _fromAction);
    320   for (ActionQueue_t::iterator iter = inititer; iter != actionqueue.end(); ++iter)
     318void ActionQueue::clearQueue()
     319{
     320  // free all actions contained in actionqueue
     321  for (ActionQueue_t::iterator iter = actionqueue.begin();
     322      !actionqueue.empty(); iter = actionqueue.begin()) {
    321323    delete *iter;
    322   actionqueue.erase(inititer, actionqueue.end());
    323   LOG(1, "There are " << actionqueue.size() << " remaining Actions.");
    324 #ifdef HAVE_ACTION_THREAD
    325   CurrentAction = actionqueue.size();
    326   mtx_queue.unlock();
    327 #endif
    328 }
    329 
    330 #ifdef HAVE_ACTION_THREAD
    331 void ActionQueue::clearTempQueue()
    332 {
     324    actionqueue.erase(iter);
     325  }
    333326  // free all actions contained in tempqueue
    334327  for (ActionQueue_t::iterator iter = tempqueue.begin();
    … …  
    337330    tempqueue.erase(iter);
    338331  }
    339 }
    340 
    341 void ActionQueue::setRunThreadIdle(const bool _flag)
    342 {
     332#ifdef HAVE_ACTION_THREAD
    343333  {
    344334    boost::unique_lock<boost::mutex> lock(mtx_idle);
    345     run_thread_isIdle = _flag;
    346   }
    347 }
    348 #endif
     335    run_thread_isIdle = true;
     336  }
     337#endif
     338}
    349339
    350340const ActionQueue::ActionTokens_t ActionQueue::getListOfActions() const
    … …  
    365355}
    366356
    367 bool ActionQueue::canUndo() const
    368 {
    369   return history->hasUndo();
    370 }
    371 
    372357void ActionQueue::redoLast()
    373358{
    … …  
    375360}
    376361
    377 bool ActionQueue::canRedo() const
    378 {
    379   return history->hasRedo();
    380 }
    381 
    382362
    383363CONSTRUCT_SINGLETON(ActionQueue)

  • src/Actions/ActionQueue.hpp

    r0ac85c3 r7b38d3  
    145145  void redoLast();
    146146
    147   /** Checks whether there is one completed Action stored in ActionHistory in the past.
    148    *
    149    * @return true - at least one Action to undo present, false - else
    150    */
    151   bool canUndo() const;
    152 
    153   /** Checks whether there is one completed Action stored in ActionHistory in the future.
    154    *
    155    * @return true - at least one Action to redo present, false - else
    156    */
    157   bool canRedo() const;
    158 
    159147  /** Return status of last executed action.
    160148   *
    … …  
    202190  void clear();
    203191
    204   /** Clears all actions present in the actionqueues from \a _fromAction.
    205    *
    206    * @param _fromAction 0 if all Actions to clear or else
    207    */
    208   void clearQueue(const size_t _fromAction = 0);
    209 
    210 #ifdef HAVE_ACTION_THREAD
    211 
    212   /** Clears the temporary queue.
    213    *
    214    */
    215   void clearTempQueue();
    216 
    217   /** Sets the run_thread_isIdle flag.
    218    *
    219    * @param _flag state to set to
    220    */
    221   void setRunThreadIdle(const bool _flag);
    222 
     192  /** Clears all actions currently present in the actionqueues.
     193   *
     194   */
     195  void clearQueue();
     196
     197#ifdef HAVE_ACTION_THREAD
    223198  /** Runs the ActionQueue.
    224199   *
    … …  
    239214   */
    240215  void wait();
    241 
    242   /** Moves all action from tempqueue into real queue.
    243    *
    244    */
    245   void insertTempQueue();
    246 
    247216#endif
    248217
    … …  
    255224  void insertAction(Action *_action, enum Action::QueryOptions state);
    256225
     226  /** Moves all action from tempqueue into real queue.
     227   *
     228   */
     229  void insertTempQueue();
     230
    257231private:
    258232  /** Private cstor for ActionQueue.
    … …  
    281255  ActionQueue_t actionqueue;
    282256
     257  //!> point to current action in actionqueue
     258  size_t CurrentAction;
     259
     260  //!> internal temporary actionqueue of actions used by insertAction()
     261  ActionQueue_t tempqueue;
     262
    283263  //!> indicates that the last action has failed
    284264  bool lastActionOk;
    285265
    286266#ifdef HAVE_ACTION_THREAD
    287   //!> point to current action in actionqueue
    288   size_t CurrentAction;
    289 
    290   //!> internal temporary actionqueue of actions used by insertAction()
    291   ActionQueue_t tempqueue;
    292 
    293267  //!> internal thread to call Actions
    294268  boost::thread run_thread;

  • src/Actions/ActionRegistry.cpp

    r0ac85c3 r7b38d3  
    9191    MakroAction * presentAction =
    9292        dynamic_cast<MakroAction *>(getActionByName("subgraph-dissection"));
    93     ASSERT( presentAction != NULL,
    94         "ActionRegistry::fillRegistry() - makro action has not been registered.");
    95     presentAction->unprepare(*this);
    96   }
    97   {
    98     MakroAction * presentAction =
    99         dynamic_cast<MakroAction *>(getActionByName("translate-molecules"));
    10093    ASSERT( presentAction != NULL,
    10194        "ActionRegistry::fillRegistry() - makro action has not been registered.");
    … …  
    143136    MakroAction * presentAction =
    144137        dynamic_cast<MakroAction *>(getActionByName("optimize-structure"));
    145     ASSERT( presentAction != NULL,
    146         "ActionRegistry::fillRegistry() - makro action has not been registered.");
    147     presentAction->prepare(*this);
    148   }
    149   {
    150     MakroAction * presentAction =
    151         dynamic_cast<MakroAction *>(getActionByName("translate-molecules"));
    152138    ASSERT( presentAction != NULL,
    153139        "ActionRegistry::fillRegistry() - makro action has not been registered.");

  • src/Actions/AtomAction/TranslateAction.def

    r0ac85c3 r7b38d3  
    1616// "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
    1717#define paramtypes (Vector)(bool)
    18 #define paramtokens ("position")("periodic")
     18#define paramtokens ("translate-atoms")("periodic")
    1919#define paramdescriptions ("translation vector")("system is constraint to periodic boundary conditions")
    2020#define paramreferences (x)(periodic)

  • src/Actions/FillAction/SuspendInMoleculeAction.cpp

    r0ac85c3 r7b38d3  
    129129  filler->CenterEdge();
    130130
     131  /// first we need to calculate some volumes and masses
    131132  std::vector<molecule *> molecules = World::getInstance().getAllMolecules();
    132   if (molecules.size() < 2) {
    133     STATUS("There must be at least two molecules: filler and to be suspended.");
    134     return Action::failure;
    135   }
    136 
    137   /// first we need to calculate some volumes and masses
    138133  double totalmass = 0.;
    139134  const bool IsAngstroem = true;
    … …  
    144139      iter != molecules.end(); ++iter)
    145140  {
    146     // skip the filler
    147     if (*iter == filler)
    148       continue;
    149141    molecule & mol = **iter;
    150142    const double mass = calculateMass(mol);
    … …  
    160152  LOG(1, "INFO: The average density is " << setprecision(10)
    161153      << totalmass / clustervolume << " atomicmassunit/"
    162       << (IsAngstroem ? " angstrom" : " atomiclength") << "^3.");
    163   if ( ((totalmass / clustervolume < 1.) && (params.density.get() > 1.))
    164       || ((totalmass / clustervolume > 1.) && (params.density.get() < 1.))) {
    165     STATUS("Desired and present molecular densities must both be either in [0,1) or in (1, inf).");
    166     return Action::failure;
    167   }
     154      << (IsAngstroem ? "angstrom" : "atomiclength") << "^3.");
    168155
    169156  // calculate maximum solvent density
    170157  std::vector<double> fillerdiameters(NDIM, 0.);
    171   const double fillervolume = calculateEnvelopeVolume(*filler, fillerdiameters);
    172   const double fillermass = calculateMass(*filler);
    173   LOG(1, "INFO: The filler's mass is " << setprecision(10)
    174       << fillermass << " atomicmassunit, and it's volume is "
    175       << fillervolume << (IsAngstroem ? " angstrom" : " atomiclength") << "^3.");
    176   const double solventdensity = fillermass / fillervolume;
     158  const double solventdensity =
     159      calculateMass(*filler) / calculateEnvelopeVolume(*filler, fillerdiameters);
     160
     161  std::vector<unsigned int> counts(3, 0);
     162  Vector offset(.5,.5,.5);
    177163
    178164  /// solve cubic polynomial
    179165  double cellvolume = 0.;
    180166  LOG(1, "Solving equidistant suspension in water problem ...");
    181   // s = solvent, f = filler, 0 = initial molecules/cluster
    182   // v_s = v_0 + v_f, m_s = m_0 + rho_f * v_f --> rho_s = m_s/v_s ==> v_f = (m_0 - rho_s * v_o) / (rho_s - rho_f)
    183   cellvolume = (totalmass - params.density.get() * clustervolume) / (params.density.get() - 1.) + clustervolume;
     167  cellvolume = (totalmass / solventdensity
     168      - (totalmass / clustervolume)) / (params.density.get() - 1.);
    184169  LOG(1, "Cellvolume needed for a density of " << params.density.get()
    185170      << " g/cm^3 is " << cellvolume << " angstroem^3.");
    … …  
    188173      (GreatestDiameter[0] * GreatestDiameter[1] * GreatestDiameter[2]);
    189174  LOG(1, "Minimum volume of the convex envelope contained in a rectangular box is "
    190       << minimumvolume << " angstrom^3.");
     175      << minimumvolume << "angstrom^3.");
    191176
    192177  if (minimumvolume > cellvolume) {
    … …  
    202187        + GreatestDiameter[1] * GreatestDiameter[2];
    203188    BoxLengths[2] = minimumvolume - cellvolume;
    204     std::vector<double> x(3, 0.);
     189    double x0 = 0.;
     190    double x1 = 0.;
     191    double x2 = 0.;
    205192    // for cubic polynomial there are either 1 or 3 unique solutions
    206     if (gsl_poly_solve_cubic(BoxLengths[0], BoxLengths[1], BoxLengths[2], &x[0], &x[1], &x[2]) == 1) {
    207       x[1] = x[0];
    208       x[2] = x[0];
    209     } else {
    210       std::swap(x[0], x[2]); // sorted in ascending order
    211     }
    212     LOG(0, "RESULT: The resulting spacing is: " << x << " .");
     193    if (gsl_poly_solve_cubic(BoxLengths[0], BoxLengths[1], BoxLengths[2], &x0, &x1, &x2) == 1)
     194      LOG(0, "RESULT: The resulting spacing is: " << x0 << " .");
     195    else {
     196      LOG(0, "RESULT: The resulting spacings are: " << x0 << " and " << x1 << " and " << x2 << " .");
     197      std::swap(x0, x2); // sorted in ascending order
     198    }
    213199
    214200    cellvolume = 1.;
    215201    for (size_t i = 0; i < NDIM; ++i) {
    216       BoxLengths[i] = x[i] + GreatestDiameter[i];
     202      BoxLengths[i] = x0 + GreatestDiameter[i];
    217203      cellvolume *= BoxLengths[i];
    218204    }
    219   }
    220 
    221   // TODO: Determine counts from resulting mass correctly (hard problem due to integers)
    222   std::vector<unsigned int> counts(3, 0);
    223   const unsigned int totalcounts = round(params.density.get() * cellvolume - totalmass) / fillermass;
    224   if (totalcounts > 0) {
    225     counts[0] = ceil(BoxLengths[0]/3.1);
    226     counts[1] = ceil(BoxLengths[1]/3.1);
    227     counts[2] = ceil(BoxLengths[2]/3.1);
     205
     206    // set new box dimensions
     207    LOG(0, "Translating to box with these boundaries.");
     208    {
     209      RealSpaceMatrix domain;
     210      for(size_t i =0; i<NDIM;++i)
     211        domain.at(i,i) = BoxLengths[i];
     212      World::getInstance().setDomain(domain);
     213    }
     214//    mol->CenterInBox();
    228215  }
    229216
    … …  
    244231      params.RandMoleculeDisplacement.get(),
    245232      params.DoRotate.get());
    246   Vector offset(.5,.5,.5);
    247233  filler_preparator.addCubeMesh(
    248234      counts,

  • src/Actions/FillAction/SuspendInMoleculeAction.def

    r0ac85c3 r7b38d3  
    1717#include "Parameters/Validators/RangeValidator.hpp"
    1818#include "Parameters/Validators/STLVectorValidator.hpp"
    19 #include "Parameters/Validators/Ops_Validator.hpp"
    2019#include "Parameters/Validators/Specific/BoxLengthValidator.hpp"
    2120#include "Parameters/Validators/Specific/VectorZeroOneComponentsValidator.hpp"
    … …  
    2625#define paramtypes (double)(double)(double)(double)(bool)
    2726#define paramtokens ("density")("min-distance")("random-atom-displacement")("random-molecule-displacement")("DoRotate")
    28 #define paramdescriptions ("desired density for the total domain, unequal 1.")("minimum distance of water molecules to present atoms")("magnitude of random atom displacement")("magnitude of random molecule displacement")("whether to rotate or not")
     27#define paramdescriptions ("desired density for the total domain")("minimum distance of water molecules to present atoms")("magnitude of random atom displacement")("magnitude of random molecule displacement")("whether to rotate or not")
    2928#define paramdefaults (PARAM_DEFAULT(1.))(PARAM_DEFAULT(1.))(PARAM_DEFAULT(0.))(PARAM_DEFAULT(0.))(PARAM_DEFAULT(false))
    3029#define paramreferences (density)(mindistance)(RandAtomDisplacement)(RandMoleculeDisplacement)(DoRotate)
    3130#define paramvalids \
    32 (RangeValidator< double >(0., 1. - std::numeric_limits<double>::epsilon()) || RangeValidator< double >(1. + std::numeric_limits<double>::epsilon(), std::numeric_limits<double>::max())) \
     31(RangeValidator< double >(0., std::numeric_limits<double>::max())) \
    3332(BoxLengthValidator()) \
    3433(BoxLengthValidator()) \

  • src/Actions/GlobalListOfActions.hpp

    r0ac85c3 r7b38d3  
    7676  (MoleculeLinearInterpolationofTrajectories) \
    7777  (MoleculeLoad) \
    78   (MoleculeRemove) \
    7978  (MoleculeRotateAroundSelfByAngle) \
    8079  (MoleculeRotateToPrincipalAxisSystem) \
    … …  
    8483  (MoleculeSaveTemperature) \
    8584  (MoleculeStretchBond) \
    86   (MoleculeTranslate) \
    8785  (MoleculeVerletIntegration) \
    8886  (PotentialFitParticleCharges) \
    … …  
    128126  (SelectionNotMoleculeByOrder) \
    129127  (SelectionNotShapeByName) \
    130   (SelectionPopAtoms) \
    131   (SelectionPushAtoms) \
    132   (SelectionPopMolecules) \
    133   (SelectionPushMolecules) \
    134128  (SelectionShapeByName) \
    135129  (ShapeCombineShapes) \

  • src/Actions/GraphAction/SubgraphDissectionAction.cpp

    r0ac85c3 r7b38d3  
    4242#include "Actions/GraphAction/UpdateMoleculesAction.hpp"
    4343#include "Actions/GraphAction/SubgraphDissectionAction.hpp"
    44 #include "Actions/SelectionAction/Atoms/PushAtomsAction.hpp"
    45 #include "Actions/SelectionAction/Atoms/PopAtomsAction.hpp"
    46 #include "Actions/SelectionAction/Atoms/AllAtomsAction.hpp"
    4744#include "Actions/ActionQueue.hpp"
    4845#include "Actions/ActionRegistry.hpp"
    … …  
    6360void GraphSubgraphDissectionAction::prepare(ActionRegistry &AR)
    6461{
    65   actions.addAction(AR.getActionByName(std::string("push-atom-selection")));
    6662  actions.addAction(AR.getActionByName(std::string("select-all-atoms")));
    6763  actions.addAction(AR.getActionByName(std::string("destroy-adjacency")));
    6864  actions.addAction(AR.getActionByName(std::string("create-adjacency")));
    6965  actions.addAction(AR.getActionByName(std::string("update-molecules")));
    70   actions.addAction(AR.getActionByName(std::string("pop-atom-selection")));
    7166  isPrepared = true;
    7267}
    … …  
    7974}
    8075
     76void reselectAtoms(const std::vector<atom *> &selected_atoms)
     77{
     78  World::getInstance().clearAtomSelection();
     79  for (std::vector<atom *>::const_iterator iter = selected_atoms.begin();
     80      iter != selected_atoms.end();
     81      ++iter)
     82    World::getInstance().selectAtom(*iter);
     83}
     84
    8185ActionState::ptr GraphSubgraphDissectionAction::performCall(){
     86  // we need to "emulate" that all atoms have been selected without destroying
     87  // current selection
     88  const std::vector<atom *> selected_atoms = World::getInstance().getSelectedAtoms();
    8289  ActionState::ptr state(MakroAction::performCall());
     90  reselectAtoms(selected_atoms);
    8391
    8492  return state;
    … …  
    8694
    8795ActionState::ptr GraphSubgraphDissectionAction::performUndo(ActionState::ptr _state) {
     96  // we need to "emulate" that all atoms have been selected without destroying
     97  // current selection
     98  const std::vector<atom *> selected_atoms = World::getInstance().getSelectedAtoms();
    8899  ActionState::ptr state(MakroAction::performUndo(_state));
     100  reselectAtoms(selected_atoms);
    89101
    90102  return state;
    … …  
    92104
    93105ActionState::ptr GraphSubgraphDissectionAction::performRedo(ActionState::ptr _state){
     106  // we need to "emulate" that all atoms have been selected without destroying
     107  // current selection
     108  const std::vector<atom *> selected_atoms = World::getInstance().getSelectedAtoms();
    94109  ActionState::ptr state(MakroAction::performRedo(_state));
     110  reselectAtoms(selected_atoms);
    95111
    96112  return state;

  • src/Actions/Makefile.am

    r0ac85c3 r7b38d3  
    297297  Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp \
    298298  Actions/MoleculeAction/LoadAction.cpp \
    299   Actions/MoleculeAction/RemoveAction.cpp \
    300299  Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp \
    301300  Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp \
    … …  
    305304  Actions/MoleculeAction/SaveTemperatureAction.cpp \
    306305  Actions/MoleculeAction/StretchBondAction.cpp \
    307   Actions/MoleculeAction/TranslateAction.cpp \
    308306  Actions/MoleculeAction/VerletIntegrationAction.cpp
    309307MOLECULEACTIONHEADER = \
    … …  
    315313  Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp \
    316314  Actions/MoleculeAction/LoadAction.hpp \
    317   Actions/MoleculeAction/RemoveAction.hpp \
    318315  Actions/MoleculeAction/RotateAroundSelfByAngleAction.hpp \
    319316  Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp \
    … …  
    323320  Actions/MoleculeAction/SaveTemperatureAction.hpp \
    324321  Actions/MoleculeAction/StretchBondAction.hpp \
    325   Actions/MoleculeAction/TranslateAction.hpp \
    326322  Actions/MoleculeAction/VerletIntegrationAction.hpp
    327323MOLECULEACTIONDEFS = \
    … …  
    333329  Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def \
    334330  Actions/MoleculeAction/LoadAction.def \
    335   Actions/MoleculeAction/RemoveAction.def \
    336331  Actions/MoleculeAction/RotateAroundSelfByAngleAction.def \
    337332  Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def \
    … …  
    341336  Actions/MoleculeAction/SaveTemperatureAction.def \
    342337  Actions/MoleculeAction/StretchBondAction.def \
    343   Actions/MoleculeAction/TranslateAction.def \
    344338  Actions/MoleculeAction/VerletIntegrationAction.def
    345339
    … …  
    418412  Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp \
    419413  Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp \
    420   Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp \
    421   Actions/SelectionAction/Atoms/PopAtomsAction.cpp \
    422   Actions/SelectionAction/Atoms/PushAtomsAction.cpp
     414  Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp
    423415SELECTIONATOMACTIONHEADER = \
    424416  Actions/SelectionAction/Atoms/AllAtomsAction.hpp \
    … …  
    435427  Actions/SelectionAction/Atoms/NotAtomByElementAction.hpp \
    436428  Actions/SelectionAction/Atoms/NotAtomByIdAction.hpp \
    437   Actions/SelectionAction/Atoms/NotAtomByOrderAction.hpp \
    438   Actions/SelectionAction/Atoms/PopAtomsAction.hpp \
    439   Actions/SelectionAction/Atoms/PushAtomsAction.hpp
     429  Actions/SelectionAction/Atoms/NotAtomByOrderAction.hpp
    440430SELECTIONATOMACTIONDEFS = \
    441431  Actions/SelectionAction/Atoms/AllAtomsAction.def \
    … …  
    452442  Actions/SelectionAction/Atoms/NotAtomByElementAction.def \
    453443  Actions/SelectionAction/Atoms/NotAtomByIdAction.def \
    454   Actions/SelectionAction/Atoms/NotAtomByOrderAction.def \
    455   Actions/SelectionAction/Atoms/PopAtomsAction.def \
    456   Actions/SelectionAction/Atoms/PushAtomsAction.def
     444  Actions/SelectionAction/Atoms/NotAtomByOrderAction.def
    457445
    458446SELECTIONMOLECULEACTIONSOURCE = \
    … …  
    470458  Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp \
    471459  Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp \
    472   Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp \
    473   Actions/SelectionAction/Molecules/PopMoleculesAction.cpp \
    474   Actions/SelectionAction/Molecules/PushMoleculesAction.cpp
     460  Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp
    475461SELECTIONMOLECULEACTIONHEADER = \
    476462  Actions/SelectionAction/Molecules/AllMoleculesAction.hpp \
    … …  
    487473  Actions/SelectionAction/Molecules/NotMoleculeByNameAction.hpp \
    488474  Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.hpp \
    489   Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.hpp \
    490   Actions/SelectionAction/Molecules/PopMoleculesAction.hpp \
    491   Actions/SelectionAction/Molecules/PushMoleculesAction.hpp
     475  Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.hpp
    492476SELECTIONMOLECULEACTIONDEFS = \
    493477  Actions/SelectionAction/Molecules/AllMoleculesAction.def \
    … …  
    504488  Actions/SelectionAction/Molecules/NotMoleculeByNameAction.def \
    505489  Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.def \
    506   Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.def \
    507   Actions/SelectionAction/Molecules/PopMoleculesAction.def \
    508   Actions/SelectionAction/Molecules/PushMoleculesAction.def
     490  Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.def
    509491                 
    510492SELECTIONSHAPEACTIONSOURCE = \

  • src/Actions/SelectionAction/Atoms/NotAtomByIdAction.def

    r0ac85c3 r7b38d3  
    2626(STLVectorValidator< std::vector<atomId_t> >(AtomIdValidator()))
    2727
     28
    2829#define statetypes (atomids_t)
    2930#define statereferences (undoatomids)

  • src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp

    r0ac85c3 r7b38d3  
    5353/** =========== define the function ====================== */
    5454ActionState::ptr SelectionMoleculeByIdAction::performCall() {
    55 
    56   enum Sucess {
    57     NoStatus,
    58     AllMoleculesUnselected,
    59     MoleculesSelected,
    60     MoleculeMissing
    61   } status = NoStatus;
    62 
    63   const molids_t molids = params.molids.get();
    64   molids_t undomolids;
    65   undomolids.reserve(molids.size());
    66   for (molids_t::const_iterator iter = molids.begin(); iter != molids.end(); ++iter) {
    67     const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
    68     if (Walker != NULL) {
    69       if (!World::getInstance().isSelected(Walker)) {
    70         LOG(1, "Selecting mol " << Walker->getName());
    71         World::getInstance().selectMolecule(Walker);
    72         undomolids.push_back(*iter);
    73         if (status < MoleculeMissing)
    74           status = MoleculesSelected;
    75       } else {
    76         if (status == NoStatus)
    77           status = AllMoleculesUnselected;
    78       }
     55  const molecule *mol = World::getInstance().getMolecule(MoleculeById(params.molindex.get()));
     56  if (mol != NULL) {
     57    if (!World::getInstance().isSelected(mol)) {
     58      LOG(1, "Selecting molecule " << mol->name);
     59      World::getInstance().selectAllMolecules(MoleculeById(params.molindex.get()));
     60      LOG(0, World::getInstance().countSelectedMolecules() << " molecules selected.");
     61      return ActionState::ptr(new SelectionMoleculeByIdState(params));
    7962    } else {
    80       status = MoleculeMissing;
     63      return Action::success;
    8164    }
     65  } else {
     66    STATUS("Cannot find molecule by given index "+toString(params.molindex.get())+".");
     67    return Action::failure;
    8268  }
    83   LOG(0, World::getInstance().countSelectedMolecules() << " mols selected.");
    84 
    85   switch (status) {
    86     case MoleculeMissing:
    87       STATUS("Cannot find all mols with given ids.");
    88       return Action::failure;
    89       break;
    90     case AllMoleculesUnselected:
    91     case MoleculesSelected:
    92       return ActionState::ptr(new SelectionMoleculeByIdState(undomolids, params));
    93       break;
    94     default:
    95       STATUS("No mols have been selected.");
    96       return Action::failure;
    97       break;
    98   }
    99   return Action::failure;
    10069}
    10170
    … …  
    10372  SelectionMoleculeByIdState *state = assert_cast<SelectionMoleculeByIdState*>(_state.get());
    10473
    105   for (molids_t::const_iterator iter = state->undomolids.begin();
    106       iter != state->undomolids.end(); ++iter) {
    107     const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
    108     World::getInstance().unselectMolecule(Walker);
    109   }
     74  World::getInstance().unselectAllMolecules(MoleculeById(state->params.molindex.get()));
    11075
    11176  return ActionState::ptr(_state);
    … …  
    11580  SelectionMoleculeByIdState *state = assert_cast<SelectionMoleculeByIdState*>(_state.get());
    11681
    117   for (molids_t::const_iterator iter = state->undomolids.begin();
    118       iter != state->undomolids.end(); ++iter) {
    119     const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
    120     World::getInstance().selectMolecule(Walker);
    121   }
     82  World::getInstance().selectAllMolecules(MoleculeById(state->params.molindex.get()));
    12283
    12384  return ActionState::ptr(_state);

  • src/Actions/SelectionAction/Molecules/MoleculeByIdAction.def

    r0ac85c3 r7b38d3  
    77
    88// all includes and forward declarations necessary for non-integral types below
    9 #include <vector>
    109#include "types.hpp"
    1110
    12 typedef std::vector<moleculeId_t> molids_t;
    13 
    14 #include "Parameters/Validators/STLVectorValidator.hpp"
    1511#include "Parameters/Validators/Specific/MoleculeIdValidator.hpp"
    1612
    … …  
    1814// ValueStorage by the token "Z" -> first column: int, Z, "Z"
    1915// "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
    20 #define paramtypes (molids_t)
     16#define paramtypes (moleculeId_t)
    2117#define paramtokens ("select-molecule-by-id")
    22 #define paramdescriptions ("molecule indices to select")
     18#define paramdescriptions ("molecule index")
    2319#undef paramdefaults
    24 #define paramreferences (molids)
     20#define paramreferences (molindex)
    2521#define paramvalids \
    26 (STLVectorValidator< std::vector<moleculeId_t> >(MoleculeIdValidator()))
     22(MoleculeIdValidator())
    2723
    28 #define statetypes (molids_t)
    29 #define statereferences (undomolids)
     24#undef statetypes
     25#undef statereferences
    3026
    3127// some defines for all the names, you may use ACTION, STATE and PARAMS

  • src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp

    r0ac85c3 r7b38d3  
    5353/** =========== define the function ====================== */
    5454ActionState::ptr SelectionNotMoleculeByIdAction::performCall() {
    55   enum Sucess {
    56     NoStatus,
    57     AllMoleculesSelected,
    58     MoleculesUnselected,
    59     MoleculeMissing
    60   } status = NoStatus;
    61 
    62   const molids_t molids = params.molids.get();
    63   molids_t undomolids;
    64   undomolids.reserve(molids.size());
    65   for (molids_t::const_iterator iter = molids.begin(); iter != molids.end(); ++iter) {
    66     const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
    67     if (Walker != NULL) {
    68       if (World::getInstance().isSelected(Walker)) {
    69         LOG(1, "Unselecting mol " << Walker->getName());
    70         World::getInstance().unselectMolecule(Walker);
    71         undomolids.push_back(*iter);
    72         if (status < MoleculeMissing)
    73           status = MoleculesUnselected;
    74       } else {
    75         if (status == NoStatus)
    76           status = AllMoleculesSelected;
    77       }
     55  const molecule *mol = World::getInstance().getMolecule(MoleculeById(params.molindex.get()));
     56  if (mol != NULL) {
     57    if (World::getInstance().isSelected(mol)) {
     58      LOG(1, "Unselecting molecule " << mol->name);
     59      World::getInstance().unselectAllMolecules(MoleculeById(params.molindex.get()));
     60      LOG(0, World::getInstance().countSelectedMolecules() << " molecules remain selected.");
     61      return ActionState::ptr(new SelectionNotMoleculeByIdState(params));
    7862    } else {
    79       status = MoleculeMissing;
     63      return Action::success;
    8064    }
     65  } else {
     66    STATUS("Cannot find molecule by given index "+toString(params.molindex.get())+".");
     67    return Action::failure;
    8168  }
    82   LOG(0, World::getInstance().countSelectedMolecules() << " mols remain selected.");
    83 
    84   switch (status) {
    85     case MoleculeMissing:
    86       STATUS("Cannot find all mols by given ids.");
    87       return Action::failure;
    88       break;
    89     case AllMoleculesSelected:
    90     case MoleculesUnselected:
    91       return ActionState::ptr(new SelectionNotMoleculeByIdState(undomolids, params));
    92       break;
    93     default:
    94       STATUS("No mols have been selected.");
    95       return Action::failure;
    96       break;
    97   }
    98   return Action::failure;
    9969}
    10070
    … …  
    10272  SelectionNotMoleculeByIdState *state = assert_cast<SelectionNotMoleculeByIdState*>(_state.get());
    10373
    104   for (molids_t::const_iterator iter = state->undomolids.begin();
    105       iter != state->undomolids.end(); ++iter) {
    106     const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
    107     World::getInstance().selectMolecule(Walker);
    108   }
     74  World::getInstance().selectAllMolecules(MoleculeById(state->params.molindex.get()));
    10975
    11076  return ActionState::ptr(_state);
    … …  
    11480  SelectionNotMoleculeByIdState *state = assert_cast<SelectionNotMoleculeByIdState*>(_state.get());
    11581
    116   for (molids_t::const_iterator iter = state->undomolids.begin();
    117       iter != state->undomolids.end(); ++iter) {
    118     const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
    119     World::getInstance().unselectMolecule(Walker);
    120   }
     82  World::getInstance().unselectAllMolecules(MoleculeById(state->params.molindex.get()));
    12183
    12284  return ActionState::ptr(_state);

  • src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.def

    r0ac85c3 r7b38d3  
    77
    88// all includes and forward declarations necessary for non-integral types below
    9 #include <vector>
    109#include "types.hpp"
    1110
    12 typedef std::vector<moleculeId_t> molids_t;
    13 
    14 #include "Parameters/Validators/STLVectorValidator.hpp"
    1511#include "Parameters/Validators/Specific/MoleculeIdValidator.hpp"
    1612
    … …  
    1814// ValueStorage by the token "Z" -> first column: int, Z, "Z"
    1915// "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
    20 #define paramtypes (molids_t)
     16#define paramtypes (moleculeId_t)
    2117#define paramtokens ("unselect-molecule-by-id")
    22 #define paramdescriptions ("molecule indices to unselect")
     18#define paramdescriptions ("molecule index")
    2319#undef paramdefaults
    24 #define paramreferences (molids)
     20#define paramreferences (molindex)
    2521#define paramvalids \
    26 (STLVectorValidator< std::vector<moleculeId_t> >(MoleculeIdValidator()))
     22(MoleculeIdValidator())
    2723
    28 #define statetypes (molids_t)
    29 #define statereferences (undomolids)
     24#undef statetypes
     25#undef statereferences
    3026
    3127// some defines for all the names, you may use ACTION, STATE and PARAMS

  • src/Actions/UndoRedoHelpers.cpp

    r0ac85c3 r7b38d3  
    5252#include "WorldTime.hpp"
    5353
    54 bool MoleCuilder::AddAtomsFromAtomicInfo(const std::vector<AtomicInfo> &atoms)
     54bool MoleCuilder::AddAtomsFromAtomicInfo(std::vector<AtomicInfo> &atoms)
    5555{
    5656  size_t i=0;
    … …  
    6969    for (size_t j=0;j<i;++j)
    7070      World::getInstance().destroyAtom(atoms[j].getId());
    71     // and announce the failure
    72     return false;
    73   }
    74   return true;
    75 }
    76 
    77 bool MoleCuilder::AddMoleculesFromAtomicInfo(std::map< moleculeId_t, std::vector<AtomicInfo> > &mol_atoms)
    78 {
    79   bool status = true;
    80   for (std::map< moleculeId_t, std::vector<AtomicInfo> >::const_iterator iter = mol_atoms.begin();
    81       iter != mol_atoms.end(); ++iter) {
    82     // re-create the atom
    83     LOG(3, "DEBUG: Re-adding molecule " << iter->first << ".");
    84     molecule *mol_Walker = World::getInstance().createMolecule();
    85 
    86     // reset the mol id
    87     bool status = true;
    88     if (mol_Walker->getId() != iter->first)
    89       status &= mol_Walker->changeId(iter->first);
    90 
    91     // add all its atoms
    92     status &= AddAtomsFromAtomicInfo(iter->second);
    93   }
    94   if (!status) {
    95     // remove all molecules again
    96     for (std::map< moleculeId_t, std::vector<AtomicInfo> >::const_iterator iter = mol_atoms.begin();
    97         iter != mol_atoms.end(); ++iter) {
    98       molecule * mol = World::getInstance().getMolecule(MoleculeById(iter->first));
    99       if (mol != NULL)
    100         removeAtomsinMolecule(mol);
    101     }
    10271    // and announce the failure
    10372    return false;
    … …  
    204173  for (std::vector<moleculeId_t>::const_iterator iter = ids.begin();
    205174      iter != ids.end(); ++iter) {
    206     molecule * mol = World::getInstance().getMolecule(MoleculeById(*iter));
     175    molecule * const mol = World::getInstance().getMolecule(MoleculeById(*iter));
    207176    if (mol != NULL) {
    208       removeAtomsinMolecule(mol);
    209       // molecules are automatically removed when empty
     177      mol->removeAtomsinMolecule();
     178      World::getInstance().destroyMolecule(mol);
    210179    }
    211180  }

  • src/Actions/UndoRedoHelpers.hpp

    r0ac85c3 r7b38d3  
    2727   * @return restoral was successful, at least atom could not be restored.
    2828   */
    29   bool AddAtomsFromAtomicInfo(const std::vector<AtomicInfo> &atoms);
    30 
    31   /** Adds removed molecules with their atoms back to the world.
    32    *
    33    * @param mol_atoms map of molecules with ids and their atoms as AtomicInfo
    34    * \return true - restoral was successful, at least one atom or molecule could not be restored
    35    */
    36   bool AddMoleculesFromAtomicInfo(std::map< moleculeId_t, std::vector<AtomicInfo> > &mol_atoms);
     29  bool AddAtomsFromAtomicInfo(std::vector<AtomicInfo> &atoms);
    3730
    3831  /** Removes atoms whose state information is stored as AtomicInfo.

  • src/Actions/WorldAction/RepeatBoxAction.cpp

    r0ac85c3 r7b38d3  
    147147      iter != allmolecules.end();
    148148      ++iter) {
    149     if (state->oldmolecules.find(*iter) == state->oldmolecules.end())
    150       removeAtomsinMolecule(*iter);
     149    if (state->oldmolecules.find(*iter) == state->oldmolecules.end()) {
     150      (*iter)->removeAtomsinMolecule();
     151      // TODO: Remove this when World don't has deprecated MoleculeListClass anymore
     152      molecules->erase(*iter);
     153      World::getInstance().destroyMolecule(*iter);
     154    }
    151155  }
    152156

  • src/Atom/atom.cpp

    r0ac85c3 r7b38d3  
    270270  removeFromMolecule();
    271271  mol = _mol;
    272   if ((mol) && (!mol->containsAtom(this))) {
    273     signOn(mol, AtomObservable::PositionChanged);
     272  if ((mol) && (!mol->containsAtom(this)))
    274273    mol->insert(this);
    275   }
    276274}
    277275
    … …  
    281279  ASSERT(!mol->containsAtom(this),
    282280      "atom::unsetMolecule() - old molecule "+toString(mol)+" still contains us!");
    283   signOff(mol, AtomObservable::PositionChanged);
    284281  mol = NULL;
    285282}
    … …  
    292289  if(mol){
    293290    if(mol->containsAtom(this)){
    294       signOff(mol, AtomObservable::PositionChanged);
    295291      mol->erase(this);
    296292    }

  • src/Fragmentation/Exporters/ExportGraph.cpp

    r0ac85c3 r7b38d3  
    8080    // remove copied atoms and molecule again
    8181    molecule *mol = *iter;
     82    mol->removeAtomsinMolecule();
     83    World::getInstance().destroyMolecule(mol);
    8284    BondFragments.ListOfMolecules.erase(iter);
    83     removeAtomsinMolecule(mol);
    8485  }
    8586}

  • src/Graph/DepthFirstSearchAnalysis.cpp

    r0ac85c3 r7b38d3  
    431431      World::getInstance().getMoleculeIter() != World::getInstance().moleculeEnd();
    432432      iter = World::getInstance().getMoleculeIter()) {
    433     // TODO: remove when deprecated MoleculeListClass is gone
    434433    World::getInstance().getMolecules()->erase(*iter);
    435434    World::getInstance().destroyMolecule(*iter);

  • src/Graph/unittests/AdjacencyListUnitTest.cpp

    r0ac85c3 r7b38d3  
    153153
    154154  // destroy molecule and contained atoms
    155   removeAtomsinMolecule(TestMolecule);
     155  TestMolecule->removeAtomsinMolecule();
     156  World::getInstance().destroyMolecule(TestMolecule);
    156157  // destroy World
    157158  World::purgeInstance();

  • src/MoleculeLeafClass.cpp

    r0ac85c3 r7b38d3  
    8585  //  }
    8686  // remove the leaf itself
    87   if (Leaf != NULL)
    88     removeAtomsinMolecule(Leaf);
     87  if (Leaf != NULL) {
     88    Leaf->removeAtomsinMolecule();
     89    World::getInstance().destroyMolecule(Leaf);
     90    Leaf = NULL;
     91  }
    8992  // remove this Leaf from level list
    9093  if (previous != NULL)

  • src/UIElements/CommandLineUI/CommandLineParser.cpp

    r0ac85c3 r7b38d3  
    443443    // force action queue to stop thread
    444444    ActionQueue::getInstance().stop();
    445     ActionQueue::getInstance().clearTempQueue();
    446445#endif
    447446    ActionQueue::getInstance().clearQueue();

  • src/UIElements/Qt4/QtMainWindow.cpp

    r0ac85c3 r7b38d3  
    146146  settings.endGroup();
    147147
    148   qRegisterMetaType<moleculeId_t>("moleculeId_t");
    149 
    150   connect(glWorldView,SIGNAL(hoverChanged(const atom&)), infoBox,SLOT(atomHover(const atom&)));
    151   connect(glWorldView,SIGNAL(hoverChanged(const molecule&, int)), infoBox,SLOT(moleculeHover(const molecule&)));
    152   connect(moleculeList,SIGNAL(moleculesVisibilityChanged(const moleculeId_t,bool)), glWorldView, SIGNAL(moleculesVisibilityChanged(const moleculeId_t,bool)));
     148  connect(glWorldView,SIGNAL(hoverChanged(const atom*)), infoBox,SLOT(atomHover(const atom*)));
    153149}
    154150

  • src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp

    r0ac85c3 r7b38d3  
    6262QGLMaterial *GLMoleculeObject::m_selectionBoxMaterial = NULL;
    6363
    64 QGLSceneNode *GLMoleculeObject::meshEmpty[GLMoleculeObject::DETAILTYPES_MAX];
    65 QGLSceneNode *GLMoleculeObject::meshSphere[GLMoleculeObject::DETAILTYPES_MAX];
    66 QGLSceneNode *GLMoleculeObject::meshCylinder[GLMoleculeObject::DETAILTYPES_MAX];
    6764
    6865double GLMoleculeObject::detailMinDistance[GLMoleculeObject::DETAILTYPES_MAX] = {0, 15, 30, 42};
    … …  
    7269{
    7370   //mesh->setParent(this);
    74   for (int i=0;i<DETAILTYPES_MAX;i++)
    75     m_mesh[i] = mesh[i];
    76   MeshFreeType = free_none;
    77    m_scaleX = 1.0f;
    78    m_scaleY = 1.0f;
    79    m_scaleZ = 1.0f;
    80    m_rotationAngle = 0.0f;
    81    m_effect = 0;
    82    m_objectId = -1;
    83    m_hovering = false;
    84    m_selected = false;
    85    m_visible = true;
    86    m_material = 0;
    87    initStaticMaterials();
    88 }
    89 
    90 GLMoleculeObject::GLMoleculeObject(QGLSceneNode *mesh, QObject *parent)
    91    : QObject(parent)
    92 {
    93    //mesh->setParent(this);
    94   for (int i=0;i<DETAILTYPES_MAX;i++)
    95     m_mesh[i] = mesh;
    96   MeshFreeType = free_none;
     71   for (int i=0;i<DETAILTYPES_MAX;i++)
     72     m_mesh[i] = mesh[i];
    9773   m_scaleX = 1.0f;
    9874   m_scaleY = 1.0f;
    … …  
    10783}
    10884
    109 GLMoleculeObject::GLMoleculeObject(QGLAbstractScene *scene, QObject *parent)
     85GLMoleculeObject::GLMoleculeObject(QGLSceneNode *mesh, QObject *parent)
    11086   : QObject(parent)
    11187{
    112   for (int i=0;i<DETAILTYPES_MAX;i++)
    113     m_mesh[i] = scene->mainNode();
    114   MeshFreeType = free_none;
     88   //mesh->setParent(this);
     89   for (int i=0;i<DETAILTYPES_MAX;i++)
     90     m_mesh[i] = mesh;
    11591   m_scaleX = 1.0f;
    11692   m_scaleY = 1.0f;
    … …  
    125101}
    126102
     103GLMoleculeObject::GLMoleculeObject(QGLAbstractScene *scene, QObject *parent)
     104   : QObject(parent)
     105{
     106   scene->setParent(this);
     107   for (int i=0;i<DETAILTYPES_MAX;i++)
     108     m_mesh[i] = scene->mainNode();
     109   m_scaleX = 1.0f;
     110   m_scaleY = 1.0f;
     111   m_scaleZ = 1.0f;
     112   m_rotationAngle = 0.0f;
     113   m_effect = 0;
     114   m_objectId = -1;
     115   m_hovering = false;
     116   m_selected = false;
     117   m_material = 0;
     118   initStaticMaterials();
     119}
     120
    127121GLMoleculeObject::~GLMoleculeObject()
    128122{
    … …  
    169163   painter->modelViewMatrix().push();
    170164   painter->modelViewMatrix().translate(m_position);
    171    if ((m_scaleX != 1.0f) || (m_scaleY != 1.0f) || (m_scaleZ != 1.0f))
    172      painter->modelViewMatrix().scale(m_scaleX, m_scaleY, m_scaleZ);
    173165   if (m_rotationAngle != 0.0f)
    174166     painter->modelViewMatrix().rotate(m_rotationAngle, m_rotationVector);
     167   painter->modelViewMatrix().scale(m_scaleX, m_scaleY, m_scaleZ);
    175168
    176169   // Apply the material and effect to the painter.
    … …  
    332325  }
    333326}
    334 
    335 void GLMoleculeObject::setVisible(bool value)
    336 {
    337   if (value != m_visible){
    338     m_visible = value;
    339     emit changed();
    340   }
    341 }
    342 
    343 void GLMoleculeObject::updateMesh(QGLSceneNode *mesh)
    344 {
    345   if (m_mesh[0] != NULL) {
    346     switch(MeshFreeType) {
    347     case free_all:
    348       for (int i=0;i<DETAILTYPES_MAX;i++)
    349         delete m_mesh[i];
    350       break;
    351     case free_single:
    352       delete m_mesh[0];
    353       break;
    354     default:
    355     case free_none:
    356       break;
    357     }
    358   }
    359   MeshFreeType = free_single;
    360   for (int i=0;i<DETAILTYPES_MAX;i++)
    361     m_mesh[i] = mesh;
    362 }

  • src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.hpp

    r0ac85c3 r7b38d3  
    7474   void setSelected(bool value);
    7575
    76    bool visible() const { return m_visible; }
    77    virtual void setVisible(bool value);
    78 
    7976   void initStaticMaterials();
    80    virtual void initialize(QGLView *view, QGLPainter *painter);
     77   void initialize(QGLView *view, QGLPainter *painter);
    8178   virtual void draw(QGLPainter *painter, const QVector4D &cameraPlane);
    8279   void drawSelectionBox(QGLPainter *painter);
    … …  
    9794   static void cleanMaterialMap();
    9895
    99    void updateMesh(QGLSceneNode *scene);
    100 
    10196   typedef std::map< size_t, QGLMaterial *> ElementMaterialMap;
    10297   static ElementMaterialMap ElementNoMaterialMap;
    … …  
    105100   enum{DETAIL_HIGHEST, DETAIL_HIGH, DETAIL_MEDIUM, DETAIL_LOW, DETAILTYPES_MAX} DetailType;
    106101
    107    static QGLSceneNode *meshEmpty[DETAILTYPES_MAX];
    108    static QGLSceneNode *meshSphere[DETAILTYPES_MAX];
    109    static QGLSceneNode *meshCylinder[DETAILTYPES_MAX];
    110 
    111102protected:
    112103
    … …  
    114105
    115106   QGLSceneNode *m_mesh[DETAILTYPES_MAX];
    116    enum enum_MeshFreeType {
    117      free_all,
    118      free_single,
    119      free_none
    120    } MeshFreeType;
    121107   QGLAbstractScene *m_scene;
    122108   QVector3D m_position;
    … …  
    134120   bool m_hovering;
    135121   bool m_selected;
    136    bool m_visible;
    137122};
    138123

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

    r0ac85c3 r7b38d3  
    5656  GLMoleculeObject(mesh, parent),
    5757  Observer(std::string("GLMoleculeObject_atom")+toString(_id)),
    58   atomicid(_id),
    59   uptodatePosition(false),
    60   uptodateElement(false)
     58  atomicid(_id)
    6159{
    6260  // sign on as observer (obtain non-const instance before)
    … …  
    110108    ELOG(2, "Atom with id "+toString(atomicid)+" is already gone.");
    111109  }
    112   uptodatePosition = true;
    113110}
    114111
    … …  
    144141  }
    145142  setScale( radius / 4. );
    146 
    147   uptodateElement = true;
    148143}
    149144
    … …  
    170165  // selected?
    171166  setSelected(World::getInstance().isAtomSelected(atomicid));
    172 }
    173 
    174 void GLMoleculeObject_atom::draw(QGLPainter *painter, const QVector4D &cameraPlane)
    175 {
    176   // hook to update prior to painting
    177   if (!uptodatePosition)
    178     resetPosition();
    179   if (!uptodateElement)
    180     resetElement();
    181 
    182   // call old hook to do the actual paining
    183   GLMoleculeObject::draw(painter, cameraPlane);
    184167}
    185168
    … …  
    202185    switch (notification->getChannelNo()) {
    203186      case AtomObservable::ElementChanged:
    204         uptodateElement = false;
     187        resetElement();
     188        emit changed();
    205189        break;
    206190      case AtomObservable::IndexChanged:
    … …  
    208192        break;
    209193      case AtomObservable::PositionChanged:
    210         uptodatePosition = false;
     194        resetPosition();
     195        emit changed();
    211196        break;
    212197      case AtomObservable::BondsAdded:
    … …  
    214199        const atom *_atom = World::getInstance().getAtom(AtomById(atomicid));
    215200        if (_atom != NULL) {
    216           // make sure position is up-to-date
    217           if (!uptodatePosition)
    218             resetPosition();
    219201          ASSERT(!_atom->getListOfBonds().empty(),
    220202              "GLMoleculeObject_atom::recieveNotification() - received BondsAdded but ListOfBonds is empty.");

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

    r0ac85c3 r7b38d3  
    3131  virtual ~GLMoleculeObject_atom();
    3232
    33   void draw(QGLPainter *painter, const QVector4D &cameraPlane);
    34 
    3533  // Observer functions
    3634  void update(Observable *publisher);
    … …  
    4745
    4846private:
    49   //!> grant GLMoleculeObject_molecule acess to reset functions
    50   friend class GLMoleculeObject_molecule;
     47  //!> grant GLWorldScene acess to reset functions
     48  friend class GLWorldScene;
    5149
    5250  void resetPosition();
    … …  
    5856
    5957  const atomId_t atomicid;
    60 
    61   bool uptodatePosition;
    62   bool uptodateElement;
    6358};
    6459

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

    r0ac85c3 r7b38d3  
    4343
    4444private:
    45   //!> grant GLMoleculeObject_molecule acess to reset functions
    46   friend class GLMoleculeObject_molecule;
     45  //!> grant WorldScene access to reset functions
     46  friend class GLWorldScene;
    4747
    4848  /** Recalculates the position of the cylinder representing the bond.

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

    r0ac85c3 r7b38d3  
    4141
    4242#include <Qt3D/qglscenenode.h>
    43 #include <Qt3D/qglbuilder.h>
    4443
    4544#include "CodePatterns/MemDebug.hpp"
    … …  
    5554#include "Element/element.hpp"
    5655#include "LinearAlgebra/Vector.hpp"
    57 #include "LinkedCell/PointCloudAdaptor.hpp"
    58 #include "LinkedCell/linkedcell.hpp"
    59 #include "Tesselation/tesselation.hpp"
    60 #include "Tesselation/BoundaryLineSet.hpp"
    61 #include "Tesselation/BoundaryTriangleSet.hpp"
    62 #include "Tesselation/CandidateForTesselation.hpp"
    63 #include "Atom/TesselPoint.hpp"
    6456#include "World.hpp"
    6557
    66 #include "GLMoleculeObject_atom.hpp"
    67 
    68 static QGLSceneNode *createMoleculeMesh(const molecule *molref, QObject *parent)
    69 {
    70 //  Shape shape = molref->getBoundingSphere();
    71   double minradius = 2.; // TODO: set to maximum bond length value
    72   LOG(3, "DEBUG: Molecule fits into sphere of radius " << minradius);
    73   if (minradius < 1.)
    74     minradius = 1.;
    75 
    76   QGeometryData geo;
    77   // we need at least three points for tesselation
    78   if (molref->getAtomCount() >= 3) {
    79     // Tesselate the points.
    80     Tesselation T;
    81     PointCloudAdaptor<molecule> cloud(const_cast<molecule *>(molref), molref->getName());
    82     T(cloud, minradius);
    83 
    84     // Fill the points into a Qt geometry.
    85     LinkedCell_deprecated LinkedList(cloud, minradius);
    86     std::map<int, int> indices;
    87     std::map<int, Vector> normals;
    88     int index = 0;
    89     for (PointMap::const_iterator piter = T.PointsOnBoundary.begin();
    90         piter != T.PointsOnBoundary.end(); ++piter) {
    91       const Vector &point = piter->second->getPosition();
    92       // add data to the primitive
    93       geo.appendVertex(QVector3D(point[0], point[1], point[2]));
    94       Vector normalvector;
    95       for (LineMap::const_iterator lineiter = piter->second->lines.begin();
    96           lineiter != piter->second->lines.end(); ++lineiter)
    97         for (TriangleMap::const_iterator triangleiter = lineiter->second->triangles.begin();
    98             triangleiter != lineiter->second->triangles.end(); ++triangleiter)
    99           normalvector +=
    100               triangleiter->second->NormalVector;
    101       normalvector.Normalize();
    102       geo.appendNormal(QVector3D(normalvector[0], normalvector[1], normalvector[2]));
    103       geo.appendColor(QColor(1, 1, 1, 1));
    104       geo.appendTexCoord(QVector2D(0, 0));
    105       indices.insert( std::make_pair( piter->second->getNr(), index++));
    106     }
    107 
    108     // Fill the tesselated triangles into the geometry.
    109     for (TriangleMap::const_iterator runner = T.TrianglesOnBoundary.begin();
    110         runner != T.TrianglesOnBoundary.end(); runner++) {
    111       int v[3];
    112       for (size_t i=0; i<3; ++i)
    113         v[i] = runner->second->endpoints[i]->getNr();
    114 
    115       // Sort the vertices so the triangle is clockwise (relative to the normal vector).
    116       Vector cross = T.PointsOnBoundary[v[1]]->getPosition() - T.PointsOnBoundary[v[0]]->getPosition();
    117       cross.VectorProduct(T.PointsOnBoundary[v[2]]->getPosition() - T.PointsOnBoundary[v[0]]->getPosition());
    118       if (cross.ScalarProduct(runner->second->NormalVector) > 0)
    119         geo.appendIndices(indices[v[0]], indices[v[1]], indices[v[2]]);
    120       else
    121         geo.appendIndices(indices[v[0]], indices[v[2]], indices[v[1]]);
    122     }
    123   }
    124 
    125   // Build a mesh from the geometry.
    126   QGLBuilder builder;
    127   builder.addTriangles(geo);
    128   QGLSceneNode *mesh = builder.finalizedSceneNode();
    129   return mesh;
    130 }
    131 
    132 GLMoleculeObject_molecule::GLMoleculeObject_molecule(QObject *parent, const molecule *molref) :
    133   GLMoleculeObject(createMoleculeMesh(molref, parent), parent),
     58GLMoleculeObject_molecule::GLMoleculeObject_molecule(QGLSceneNode *mesh[], QObject *parent, const molecule *molref) :
     59  GLMoleculeObject(mesh, parent),
    13460  Observer(std::string("GLMoleculeObject_molecule")+toString(molref->getId())),
    135   isBoundingBoxUptodate(true),
    136   isSignedOn(false),
    137   _molecule(molref),
    138   TesselationHullUptodate(true),
    139   hoverAtom(NULL)
     61  _molecule(molref)
    14062{
    14163  // sign on as observer (obtain non-const instance before)
    142   _molecule->signOn(this, molecule::AtomInserted);
    143   _molecule->signOn(this, molecule::AtomRemoved);
    144   _molecule->signOn(this, molecule::AtomMoved);
    145   isSignedOn = true;
    14664  /*molref->signOn(this, AtomObservable::IndexChanged);
    14765  molref->signOn(this, AtomObservable::PositionChanged);
    … …  
    15169  World::getInstance().signOn(this, World::SelectionChanged);
    15270  updateBoundingBox();
    153 
    154   // initially, atoms and bonds should be visible
    155   m_visible = false;
    156 
    157   init();
    158 
    159   connect (this, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SLOT(hoverChangedSignalled(GLMoleculeObject *)));
    160   connect (this, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SIGNAL(changed()));
    161 
    162   connect( this, SIGNAL(clicked()), this, SLOT(wasClicked()));
    163 }
    164 
    165 GLMoleculeObject_molecule::GLMoleculeObject_molecule(QGLSceneNode *mesh[], QObject *parent, const molecule *molref) :
    166   GLMoleculeObject(mesh, parent),
    167   Observer(std::string("GLMoleculeObject_molecule")+toString(molref->getId())),
    168   isBoundingBoxUptodate(true),
    169   isSignedOn(false),
    170   _molecule(molref),
    171   TesselationHullUptodate(true),
    172   hoverAtom(NULL)
    173 {
    174   // sign on as observer (obtain non-const instance before)
    175   _molecule->signOn(this, molecule::AtomInserted);
    176   _molecule->signOn(this, molecule::AtomRemoved);
    177   _molecule->signOn(this, molecule::AtomMoved);
    178   isSignedOn = true;
    179   /*molref->signOn(this, AtomObservable::IndexChanged);
    180   molref->signOn(this, AtomObservable::PositionChanged);
    181   molref->signOn(this, AtomObservable::ElementChanged);
    182   molref->signOn(this, AtomObservable::BondsAdded);*/
    183   setMaterial(getMaterial(1));
    184   World::getInstance().signOn(this, World::SelectionChanged);
    185   updateBoundingBox();
    186 
    187   // initially, atoms and bonds should be visible
    188   m_visible = false;
    189 
    190   init();
    191 
    192   connect (this, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SLOT(hoverChangedSignalled(GLMoleculeObject *)));
    193   connect (this, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SIGNAL(changed()));
    194 
    195   connect( this, SIGNAL(clicked()), this, SLOT(wasClicked()));
    19671}
    19772
    19873GLMoleculeObject_molecule::~GLMoleculeObject_molecule()
    19974{
    200   if (isSignedOn) {
    201     _molecule->signOff(this, molecule::AtomInserted);
    202     _molecule->signOff(this, molecule::AtomRemoved);
    203     _molecule->signOff(this, molecule::AtomMoved);
    204   }
    20575  /*_atom->signOff(this, AtomObservable::IndexChanged);
    20676  _atom->signOff(this, AtomObservable::PositionChanged);
    … …  
    21080}
    21181
    212 /** Initialise the WorldScene with molecules and atoms from World.
    213  *
    214  */
    215 void GLMoleculeObject_molecule::init()
    216 {
    217   if (_molecule->begin() != _molecule->end()) {
    218     int atomicid = -1;
    219     for (molecule::const_iterator atomiter = _molecule->begin();
    220         atomiter != _molecule->end();
    221         atomiter++) {
    222       // create atom objects in scene
    223       atomicid = (*atomiter)->getId();
    224       atomInserted(atomicid);
    225 
    226       // create bond objects in scene
    227       const BondList &bondlist = (*atomiter)->getListOfBonds();
    228       for (BondList::const_iterator bonditer = bondlist.begin();
    229           bonditer != bondlist.end();
    230           ++bonditer) {
    231         const bond::ptr _bond = *bonditer;
    232         const GLMoleculeObject_bond::SideOfBond side = (_bond->leftatom == *atomiter) ?
    233             GLMoleculeObject_bond::left : GLMoleculeObject_bond::right;
    234         bondInserted(_bond, side);
    235       }
    236     }
    237     // set id to one of the atom's as either mol or atoms is present at the same time
    238     setObjectId(atomicid);
    239   }
    240 }
    241 
    242 void GLMoleculeObject_molecule::addAtomBonds(
    243     const bond::ptr &_bond,
    244     const GLMoleculeObject_bond::SideOfBond _side
    245     )
    246 {
    247   bool bond_present = false;
    248   const BondIds ids = getBondIds(_bond, _side);
    249   // check whether bond is not present already
    250   bond_present = BondsinSceneMap.count(ids);
    251   if (!bond_present)
    252     bondInserted(_bond, _side);
    253   else {
    254     BondsinSceneMap[ids]->resetPosition();
    255     BondsinSceneMap[ids]->resetWidth();
    256   }
    257 }
    258 
    259 void GLMoleculeObject_molecule::addAtomBonds(
    260     const atom *_atom)
    261 {
    262   const bool atom_present = AtomsinSceneMap.count(_atom->getId());
    263   const BondList &bondlist = _atom->getListOfBonds();
    264   for (BondList::const_iterator bonditer = bondlist.begin();
    265       (bonditer != bondlist.end()) && atom_present;
    266       ++bonditer) {
    267     const bond::ptr _bond = *bonditer;
    268     // check if OtherAtom's sphere is already present
    269     const atom *OtherAtom = _bond->GetOtherAtom(_atom);
    270     const bool otheratom_present = AtomsinSceneMap.count(OtherAtom->getId());
    271     if (otheratom_present && atom_present) {
    272       const GLMoleculeObject_bond::SideOfBond side = (_bond->leftatom == _atom) ?
    273           GLMoleculeObject_bond::left : GLMoleculeObject_bond::right;
    274       const GLMoleculeObject_bond::SideOfBond otherside = (_bond->leftatom == _atom) ?
    275           GLMoleculeObject_bond::right : GLMoleculeObject_bond::left;
    276       addAtomBonds(_bond, side);
    277       addAtomBonds(_bond, otherside);
    278     }
    279   }
    280 }
    281 
    282 void GLMoleculeObject_molecule::reinit()
    283 {
    284   if (_molecule->getAtomCount() > 0) {
    285     for (molecule::const_iterator atomiter = _molecule->begin();
    286         atomiter != _molecule->end();
    287         atomiter++) {
    288       // check whether atom already exists
    289       const atomId_t atomid = (*atomiter)->getId();
    290       const bool atom_present = AtomsinSceneMap.count(atomid);
    291       if (!atom_present)
    292         atomInserted((*atomiter)->getId());
    293       else
    294         AtomsinSceneMap[atomid]->resetPosition();
    295 
    296 
    297       // create bond objects in scene
    298       addAtomBonds(*atomiter);
    299     }
    300   }
    301 }
    302 
    30382void GLMoleculeObject_molecule::updateBoundingBox()
    30483{
    305   isBoundingBoxUptodate = true;
    30684  Shape shape = _molecule->getBoundingSphere();
    30785  Vector v = shape.getCenter();
    … …  
    31997
    32098void GLMoleculeObject_molecule::subjectKilled(Observable *publisher)
    321 {
    322   isSignedOn = false;
    323 }
     99{}
    324100
    325101void GLMoleculeObject_molecule::recieveNotification(Observable *publisher, Notification_ptr notification)
    … …  
    332108          << notification->getChannelNo() << ".";
    333109#endif
    334     switch (notification->getChannelNo()) {
    335       case molecule::AtomInserted:
    336       {
    337         const atomId_t _id = _molecule->lastChanged()->getId();
    338   #ifdef LOG_OBSERVER
    339         observerLog().addMessage() << "++ Observer " << observerLog().getName(static_cast<Observer *>(this)) << " received notification that atom "+toString(_id)+" has been inserted.";
    340   #endif
    341         TesselationHullUptodate = false;
    342         isBoundingBoxUptodate = false;
    343         atomInserted(_id);
    344         break;
    345       }
    346       case World::AtomRemoved:
    347       {
    348         const atomId_t _id = _molecule->lastChanged()->getId();
    349   #ifdef LOG_OBSERVER
    350         observerLog().addMessage() << "++ Observer " << observerLog().getName(static_cast<Observer *>(this)) << " received notification that atom "+toString(_id)+" has been removed.";
    351   #endif
    352         TesselationHullUptodate = false;
    353         isBoundingBoxUptodate = false;
    354         atomRemoved(_id);
    355         break;
    356       }
    357       case molecule::AtomMoved:
    358       {
    359   #ifdef LOG_OBSERVER
    360         const atomId_t _id = _molecule->lastChanged()->getId();
    361         observerLog().addMessage() << "++ Observer " << observerLog().getName(static_cast<Observer *>(this)) << " received notification that atom "+toString(_id)+" has been inserted.";
    362   #endif
    363         TesselationHullUptodate = false;
    364         isBoundingBoxUptodate = false;
    365         break;
    366       }
    367       default:
    368         break;
    369     }
    370110  }else{
    371111    // notification from world
    … …  
    385125}
    386126
    387 void GLMoleculeObject_molecule::initialize(QGLView *view, QGLPainter *painter)
    388 {
    389   // Initialize all of the mesh objects that we have as children.
    390   if (m_visible) {
    391     GLMoleculeObject::initialize(view, painter);
    392   } else {
    393    foreach (QObject *obj, children()) {
    394      GLMoleculeObject *meshobj = qobject_cast<GLMoleculeObject *>(obj);
    395        if (meshobj)
    396          meshobj->initialize(view, painter);
    397    }
    398   }
    399 }
    400 
    401 void GLMoleculeObject_molecule::draw(QGLPainter *painter, const QVector4D &cameraPlane)
    402 {
    403   // draw either molecule's mesh or all atoms and bonds
    404   if (m_visible) {
    405     updateTesselationHull();
    406 
    407     painter->modelViewMatrix().push();
    408 
    409     // Apply the material and effect to the painter.
    410     QGLMaterial *material;
    411     if (m_hovering)
    412         material = m_hoverMaterial;
    413     else if (m_selected)
    414         material = m_selectionMaterial;
    415     else
    416         material = m_material;
    417 
    418     ASSERT(material, "GLMoleculeObject::draw: chosen material is NULL");
    419 
    420     painter->setColor(material->diffuseColor());
    421     painter->setFaceMaterial(QGL::AllFaces, material);
    422     if (m_effect)
    423         painter->setUserEffect(m_effect);
    424     else
    425         painter->setStandardEffect(QGL::LitMaterial);
    426 
    427     // Mark the object for object picking purposes.
    428     int prevObjectId = painter->objectPickId();
    429     if (m_objectId != -1)
    430         painter->setObjectPickId(m_objectId);
    431 
    432     m_mesh[0]->draw(painter);
    433 
    434     // Turn off the user effect, if present.
    435     if (m_effect)
    436         painter->setStandardEffect(QGL::LitMaterial);
    437 
    438     // Revert to the previous object identifier.
    439     painter->setObjectPickId(prevObjectId);
    440 
    441     // Restore the modelview matrix.
    442     painter->modelViewMatrix().pop();
    443 
    444     //    GLMoleculeObject::draw(painter, cameraPlane);
    445   } else {
    446     // Draw all of the mesh objects that we have as children.
    447     foreach (QObject *obj, children()) {
    448       GLMoleculeObject *meshobj = qobject_cast<GLMoleculeObject *>(obj);
    449       if (meshobj)
    450         meshobj->draw(painter, cameraPlane);
    451     }
    452 
    453     // update bounding box prior to selection
    454     if (!isBoundingBoxUptodate)
    455       updateBoundingBox();
    456 
    457     painter->modelViewMatrix().push();
    458     painter->modelViewMatrix().translate(m_position);
    459     if ((m_scaleX != 1.0f) || (m_scaleY != 1.0f) || (m_scaleZ != 1.0f))
    460       painter->modelViewMatrix().scale(m_scaleX, m_scaleY, m_scaleZ);
    461     if (m_rotationAngle != 0.0f)
    462       painter->modelViewMatrix().rotate(m_rotationAngle, m_rotationVector);
    463 
    464     // Draw a box around the mesh, if selected.
    465     if (m_selected)
    466       drawSelectionBox(painter);
    467 
    468     // Restore the modelview matrix.
    469     painter->modelViewMatrix().pop();
    470   }
    471 }
    472 
    473 /** Adds an atom of this molecule to the scene.
    474  *
    475  * @param _atom atom to add
    476  */
    477 void GLMoleculeObject_molecule::atomInserted(const atomicNumber_t _id)
    478 {
    479   LOG(3, "INFO: GLWorldScene: Received signal atomInserted for atom "+toString(_id)+".");
    480   GLMoleculeObject_atom *atomObject = new GLMoleculeObject_atom(GLMoleculeObject::meshSphere, this, _id);
    481   AtomNodeMap::iterator iter = AtomsinSceneMap.find(_id);
    482   ASSERT(iter == AtomsinSceneMap.end(),
    483       "GLWorldScene::atomAdded() - same atom with id "+toString(_id)+" added again.");
    484   AtomsinSceneMap.insert( make_pair(_id, atomObject) );
    485 
    486   qRegisterMetaType<atomId_t>("atomId_t");
    487   qRegisterMetaType<bond::ptr>("bond::ptr");
    488   qRegisterMetaType<GLMoleculeObject_bond::SideOfBond>("GLMoleculeObject_bond::SideOfBond");
    489   connect (atomObject, SIGNAL(clicked(atomId_t)), this, SIGNAL(atomClicked(atomId_t)));
    490   connect (atomObject, SIGNAL(changed()), this, SIGNAL(changed()));
    491   connect (atomObject, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SIGNAL(changed()));
    492   connect (atomObject, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SLOT(hoverChangedSignalled(GLMoleculeObject *)));
    493   connect (atomObject, SIGNAL(selectionChanged()), this, SIGNAL(changed()));
    494   connect (atomObject, SIGNAL(BondsInserted(const bond::ptr , const GLMoleculeObject_bond::SideOfBond)), this, SLOT(bondInserted(const bond::ptr , const GLMoleculeObject_bond::SideOfBond)));
    495   connect (atomObject, SIGNAL(indexChanged(GLMoleculeObject_atom*, int, int)), this, SIGNAL(changeAtomId(GLMoleculeObject_atom*, int, int)));
    496 
    497   isBoundingBoxUptodate = false;
    498 
    499   if (m_objectId  == -1)
    500     setObjectId(_id);
    501 
    502   // add all bonds
    503   const atom *Walker = World::getInstance().getAtom(AtomById(_id));
    504   addAtomBonds(Walker);
    505 
    506   emit changeOccured();
    507 }
    508 
    509 /** Removes an atom of this molecule from the scene.
    510  *
    511  * We just the id as the atom might have already been destroyed.
    512  *
    513  * @param _id id of atom to remove
    514  */
    515 void GLMoleculeObject_molecule::atomRemoved(const atomicNumber_t _id)
    516 {
    517   LOG(3, "INFO: GLWorldScene: Received signal atomRemoved for atom "+toString(_id)+".");
    518   // bonds are removed by signal coming from ~bond
    519 
    520   if (m_objectId == _id)
    521     setObjectId(-1);
    522 
    523   // remove atoms
    524   AtomNodeMap::iterator iter = AtomsinSceneMap.find(_id);
    525   ASSERT(iter != AtomsinSceneMap.end(),
    526       "GLWorldScene::atomRemoved() - atom "+toString(_id)+" not on display.");
    527   GLMoleculeObject_atom *atomObject = iter->second;
    528   atomObject->disconnect();
    529   AtomsinSceneMap.erase(iter);
    530   delete atomObject;
    531 
    532   isBoundingBoxUptodate = false;
    533 
    534   emit changeOccured();
    535 }
    536 
    537 void GLMoleculeObject_molecule::hoverChangedSignalled(GLMoleculeObject *ob)
    538 {
    539   // Find the atom, ob corresponds to.
    540   hoverAtom = NULL;
    541   GLMoleculeObject_atom *atomObject = dynamic_cast<GLMoleculeObject_atom *>(ob);
    542   if (atomObject){
    543     for (AtomNodeMap::iterator iter = AtomsinSceneMap.begin();iter != AtomsinSceneMap.end(); ++ iter){
    544       if (iter->second == atomObject)
    545         hoverAtom = World::getInstance().getAtom(AtomById(iter->first));
    546     }
    547 
    548     // Propagate signal.
    549     emit hoverChanged(*hoverAtom);
    550   } else {
    551     // Find the atom, ob corresponds to.
    552     GLMoleculeObject_molecule *moleculeObject = dynamic_cast<GLMoleculeObject_molecule *>(ob);
    553     if (moleculeObject == this){
    554       // Propagate signal.
    555       emit hoverChanged(*_molecule, 0);
    556     }
    557   }
    558 }
    559 
    560 
    561 /** Helper function to get bond ids in the correct order for BondNodeMap.
    562  *
    563  * \return pair of ids in correct order.
    564  */
    565 GLMoleculeObject_molecule::BondIds GLMoleculeObject_molecule::getBondIds(
    566     const bond::ptr _bond,
    567     const enum GLMoleculeObject_bond::SideOfBond _side)
    568 {
    569   BondIds ids;
    570   switch (_side) {
    571     case GLMoleculeObject_bond::left:
    572       ids = std::make_pair(_bond->leftatom->getId(), _bond->rightatom->getId());
    573       break;
    574     case GLMoleculeObject_bond::right:
    575       ids = std::make_pair(_bond->rightatom->getId(), _bond->leftatom->getId());
    576       break;
    577   }
    578   return ids;
    579 }
    580 
    581 /** Adds a bond to the scene.
    582  *
    583  * @param _bond bond to add
    584  * @param side which side of the bond (left or right)
    585  */
    586 void GLMoleculeObject_molecule::bondInserted(const bond::ptr _bond, const enum GLMoleculeObject_bond::SideOfBond _side)
    587 {
    588   LOG(3, "INFO: GLWorldScene::bondInserted() - Adding bond "+toString(*_bond)+".");
    589   //LOG(4, "INFO: Currently present bonds " << BondsinSceneMap << ".");
    590 
    591   const BondIds ids = getBondIds(_bond, _side);
    592   BondNodeMap::iterator iter = BondsinSceneMap.find(ids);
    593   if (iter == BondsinSceneMap.end()) {
    594     GLMoleculeObject_bond * bondObject =
    595         new GLMoleculeObject_bond(GLMoleculeObject::meshCylinder, this, _bond, _side);
    596     connect (
    597         bondObject, SIGNAL(BondRemoved(const atomId_t, const atomId_t)),
    598         this, SLOT(bondRemoved(const atomId_t, const atomId_t)));
    599     connect (bondObject, SIGNAL(changed()), this, SIGNAL(changed()));
    600     BondsinSceneMap.insert( make_pair(ids, bondObject) );
    601   //    BondIdsinSceneMap.insert( Leftids );
    602   } else {
    603     iter->second->resetPosition();
    604     iter->second->resetWidth();
    605   }
    606   emit changeOccured();
    607 }
    608 
    609 /** Removes a bond from the scene.
    610  *
    611  * @param _bond bond to remove
    612  */
    613 void GLMoleculeObject_molecule::bondRemoved(const atomId_t leftnr, const atomId_t rightnr)
    614 {
    615   LOG(3, "INFO: GLWorldScene::bondRemoved() - Removing bond between "+toString(leftnr)+" and "+toString(rightnr)+".");
    616   {
    617     // left bond
    618     const BondIds Leftids( make_pair(leftnr, rightnr) );
    619     BondNodeMap::iterator leftiter = BondsinSceneMap.find( Leftids );
    620     ASSERT(leftiter != BondsinSceneMap.end(),
    621         "GLWorldScene::bondRemoved() - bond "+toString(leftnr)+"-"
    622         +toString(rightnr)+" not on display.");
    623     GLMoleculeObject_bond *bondObject = leftiter->second;
    624     bondObject->disconnect();
    625     BondsinSceneMap.erase(leftiter);
    626     delete bondObject; // is done by signal from bond itself
    627     //LOG(4, "INFO: Still present bonds " << BondsinSceneMap << ".");
    628   }
    629 
    630   emit changeOccured();
    631 }
    632 
    633 void GLMoleculeObject_molecule::setVisible(bool value)
    634 {
    635   // first update the mesh if we are going to be visible now
    636   if (value)
    637     updateTesselationHull();
    638   // then emit onward
    639   GLMoleculeObject::setVisible(value);
    640 }
    641 
    642 void GLMoleculeObject_molecule::updateTesselationHull()
    643 {
    644   if (!TesselationHullUptodate) {
    645     updateMesh(createMoleculeMesh(_molecule, parent()));
    646     TesselationHullUptodate = true;
    647   }
    648 }
    649 
    650 std::ostream &operator<<(std::ostream &ost, const GLMoleculeObject_molecule::BondIds &t)
    651 {
    652   ost << t.first << "," << t.second;
    653   return ost;
    654 }
    655 
    656 void GLMoleculeObject_molecule::wasClicked()
    657 {
    658   LOG(4, "INFO: GLMoleculeObject_molecule: atom " << _molecule->getId() << " has been clicked");
    659   emit moleculeClicked(_molecule->getId());
    660 }

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

    r0ac85c3 r7b38d3  
    2222class atom;
    2323class bond;
    24 class GLMoleculeObject_atom;
    25 class GLWorldScene;
    2624class molecule;
    2725
    … …  
    3028  Q_OBJECT
    3129public:
    32   GLMoleculeObject_molecule(QObject *parent, const molecule *molref);
    3330  GLMoleculeObject_molecule(QGLSceneNode *mesh[], QObject *parent, const molecule *molref);
    3431  virtual ~GLMoleculeObject_molecule();
    … …  
    4138  void recieveNotification(Observable *publisher, Notification_ptr notification);
    4239
    43   void initialize(QGLView *view, QGLPainter *painter);
    44   void draw(QGLPainter *painter, const QVector4D &cameraPlane);
    45 
    46   typedef std::pair< atomId_t, atomId_t> BondIds;
    47   friend std::ostream &operator<<(std::ostream &ost, const BondIds &t);
    48 
    49   static BondIds getBondIds(
    50       const bond::ptr _bond,
    51       const enum GLMoleculeObject_bond::SideOfBond side);
    52 
    53   void selected(const bool _isSelected)
    54   { isSelected = _isSelected; }
    55 
    56 signals:
    57   void changed();
    58   void changeOccured();
    59   void hoverChanged(const atom&);
    60   void hoverChanged(const molecule&, int);
    61   void atomClicked(atomId_t no);
    62   void moleculeClicked(moleculeId_t no);
    63   void changeAtomId(GLMoleculeObject_atom *, int, int);
    64 
    65 private slots:
    66   //!> grant GLWorldScene access to private slots
    67   friend class GLWorldScene;
    68 
    69   void wasClicked();
    70   void atomInserted(const atomicNumber_t _id);
    71   void atomRemoved(const atomicNumber_t _id);
    72   void bondInserted(const bond::ptr _bond, const GLMoleculeObject_bond::SideOfBond side);
    73   void bondRemoved(const atomId_t leftnr, const atomId_t rightnr);
    74   void hoverChangedSignalled(GLMoleculeObject *ob);
    75 
    76   void setVisible(bool value);
    77 
    7840private:
    79   void init();
    80   void reinit();
    81 
    82   void addAtomBonds(
    83       const bond::ptr &_bond,
    84       const GLMoleculeObject_bond::SideOfBond _side
    85       );
    86   void addAtomBonds(const atom *_atom);
    87 
    88   void updateTesselationHull();
    89 
    90   //!> states whether selection box is additionally drawn or not
    91   bool isSelected;
    92   bool isBoundingBoxUptodate;
    93 
    94   //!> whether we are signed on to the associated molecule
    95   bool isSignedOn;
    9641
    9742  const molecule *_molecule;
    98 
    99   bool TesselationHullUptodate;
    100 
    101   typedef std::map< atomId_t, GLMoleculeObject_atom* > AtomNodeMap;
    102   typedef std::map< BondIds , GLMoleculeObject_bond* > BondNodeMap;
    103   AtomNodeMap AtomsinSceneMap;
    104   BondNodeMap BondsinSceneMap;
    105 
    106   const atom *hoverAtom;
    10743};
    10844
    109 std::ostream &operator<<(std::ostream &ost, const GLMoleculeObject_molecule::BondIds &t);
    11045
    11146

  • src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp

    r0ac85c3 r7b38d3  
    6363typedef QGLSceneNode *MeshList[GLMoleculeObject::DETAILTYPES_MAX];
    6464
    65 static QGLSceneNode *createShapeMesh(Shape &shape, QObject *parent)
     65QGLSceneNode *createShapeMesh(Shape &shape, QObject *parent)
    6666{
    6767  size_t NumPointsonSurface = 200;

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

    r0ac85c3 r7b38d3  
    6060#include "Bond/bond.hpp"
    6161#include "Descriptors/AtomIdDescriptor.hpp"
    62 #include "Descriptors/MoleculeIdDescriptor.hpp"
    6362#include "Helpers/helpers.hpp"
    6463#include "Shapes/ShapeRegistry.hpp"
    … …  
    7069using namespace MoleCuilder;
    7170
     71std::ostream &operator<<(std::ostream &ost, const GLWorldScene::BondIds &t)
     72{
     73  ost << t.first << "," << t.second;
     74  return ost;
     75}
     76
    7277GLWorldScene::GLWorldScene(QObject *parent)
    73    : QObject(parent)
     78   : QObject(parent),
     79     hoverAtom(NULL)
    7480{
    7581  int sphereDetails[] = {5, 3, 2, 0};
    … …  
    7783  for (int i=0;i<GLMoleculeObject::DETAILTYPES_MAX;i++){
    7884    QGLBuilder emptyBuilder;
    79     GLMoleculeObject::meshEmpty[i] = emptyBuilder.finalizedSceneNode();
     85    meshEmpty[i] = emptyBuilder.finalizedSceneNode();
    8086    QGLBuilder sphereBuilder;
    8187    sphereBuilder << QGLSphere(2.0, sphereDetails[i]);
    82     GLMoleculeObject::meshSphere[i] = sphereBuilder.finalizedSceneNode();
    83     GLMoleculeObject::meshSphere[i]->setOption(QGLSceneNode::CullBoundingBox, true);
     88    meshSphere[i] = sphereBuilder.finalizedSceneNode();
     89    meshSphere[i]->setOption(QGLSceneNode::CullBoundingBox, true);
    8490    QGLBuilder cylinderBuilder;
    8591    cylinderBuilder << QGLCylinder(.25,.25,1.0,cylinderDetails[i]);
    86     GLMoleculeObject::meshCylinder[i] = cylinderBuilder.finalizedSceneNode();
    87     GLMoleculeObject::meshCylinder[i]->setOption(QGLSceneNode::CullBoundingBox, true);
     92    meshCylinder[i] = cylinderBuilder.finalizedSceneNode();
     93    meshCylinder[i]->setOption(QGLSceneNode::CullBoundingBox, true);
    8894  }
    8995
    9096  connect(this, SIGNAL(updated()), this, SLOT(update()));
    91 
    9297
    9398  setSelectionMode(SelectAtom);
    … …  
    107112void GLWorldScene::init()
    108113{
    109   const std::vector<molecule *> &molecules = World::getInstance().getAllMolecules();
    110 
    111   for (std::vector<molecule*>::const_iterator moliter = molecules.begin();
    112       moliter != molecules.end();
    113       moliter++) {
    114     // create molecule objects in scene
    115     moleculeInserted(*moliter);
     114  const std::vector<atom*> &atoms = World::getInstance().getAllAtoms();
     115
     116  if (atoms.size() > 0) {
     117    for (std::vector<atom*>::const_iterator atomiter = atoms.begin();
     118        atomiter != atoms.end();
     119        atomiter++) {
     120      // create atom objects in scene
     121      atomInserted((*atomiter)->getId());
     122
     123      // create bond objects in scene
     124      const BondList &bondlist = (*atomiter)->getListOfBonds();
     125      for (BondList::const_iterator bonditer = bondlist.begin();
     126          bonditer != bondlist.end();
     127          ++bonditer) {
     128        const bond::ptr _bond = *bonditer;
     129        const GLMoleculeObject_bond::SideOfBond side = (_bond->leftatom == *atomiter) ?
     130            GLMoleculeObject_bond::left : GLMoleculeObject_bond::right;
     131        bondInserted(_bond, side);
     132      }
     133    }
    116134  }
    117135}
    … …  
    125143void GLWorldScene::update()
    126144{
    127   const std::vector<molecule *> &molecules = World::getInstance().getAllMolecules();
    128 
    129   for (std::vector<molecule*>::const_iterator moliter = molecules.begin();
    130       moliter != molecules.end();
    131       moliter++) {
    132     // check whether molecule already exists
    133     const moleculeId_t molid = (*moliter)->getId();
    134     const bool mol_present = MoleculesinSceneMap.count(molid);
    135     if (!mol_present)
    136       moleculeInserted(*moliter);
    137   }
     145  const std::vector<atom*> &atoms = World::getInstance().getAllAtoms();
     146
     147  if (atoms.size() > 0) {
     148    for (std::vector<atom*>::const_iterator atomiter = atoms.begin();
     149        atomiter != atoms.end();
     150        atomiter++) {
     151      // check whether atom already exists
     152      const atomId_t atomid = (*atomiter)->getId();
     153      const bool atom_present = AtomsinSceneMap.count(atomid);
     154      if (!atom_present)
     155        atomInserted((*atomiter)->getId());
     156      else
     157        AtomsinSceneMap[atomid]->resetPosition();
     158
     159
     160      // create bond objects in scene
     161      const BondList &bondlist = (*atomiter)->getListOfBonds();
     162      for (BondList::const_iterator bonditer = bondlist.begin();
     163          bonditer != bondlist.end();
     164          ++bonditer) {
     165        const bond::ptr _bond = *bonditer;
     166        const GLMoleculeObject_bond::SideOfBond side = (_bond->leftatom == *atomiter) ?
     167            GLMoleculeObject_bond::left : GLMoleculeObject_bond::right;
     168        bool bond_present = false;
     169        const BondIds ids = getBondIds(_bond,side);
     170        if (atom_present) {
     171          // check whether bond is not present already
     172          bond_present = BondsinSceneMap.count(ids);
     173        }
     174        if (!bond_present)
     175          bondInserted(_bond, side);
     176        else {
     177          BondsinSceneMap[ids]->resetPosition();
     178          BondsinSceneMap[ids]->resetWidth();
     179        }
     180      }
     181    }
     182  }
     183}
     184
     185/** Adds an atom to the scene.
     186 *
     187 * @param _atom atom to add
     188 */
     189void GLWorldScene::atomInserted(const atomicNumber_t _id)
     190{
     191  LOG(3, "INFO: GLWorldScene: Received signal atomInserted for atom "+toString(_id)+".");
     192  GLMoleculeObject_atom *atomObject = new GLMoleculeObject_atom(meshSphere, this, _id);
     193  AtomNodeMap::iterator iter = AtomsinSceneMap.find(_id);
     194  ASSERT(iter == AtomsinSceneMap.end(),
     195      "GLWorldScene::atomAdded() - same atom with id "+toString(_id)+" added again.");
     196  AtomsinSceneMap.insert( make_pair(_id, atomObject) );
     197
     198  qRegisterMetaType<atomId_t>("atomId_t");
     199  qRegisterMetaType<bond::ptr>("bond::ptr");
     200  qRegisterMetaType<GLMoleculeObject_bond::SideOfBond>("GLMoleculeObject_bond::SideOfBond");
     201  connect (atomObject, SIGNAL(clicked(atomId_t)), this, SLOT(atomClicked(atomId_t)));
     202  connect (atomObject, SIGNAL(changed()), this, SIGNAL(changed()));
     203  connect (atomObject, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SIGNAL(changed()));
     204  connect (atomObject, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SLOT(hoverChangedSignalled(GLMoleculeObject *)));
     205  connect (atomObject, SIGNAL(selectionChanged()), this, SIGNAL(changed()));
     206  connect (atomObject, SIGNAL(BondsInserted(const bond::ptr , const GLMoleculeObject_bond::SideOfBond)), this, SLOT(bondInserted(const bond::ptr , const GLMoleculeObject_bond::SideOfBond)));
     207  connect (atomObject, SIGNAL(indexChanged(GLMoleculeObject_atom*, int, int)), this, SLOT(changeAtomId(GLMoleculeObject_atom*, int, int)));
     208  //bondsChanged(_atom);
     209  emit changeOccured();
     210}
     211
     212/** Removes an atom from the scene.
     213 *
     214 * We just the id as the atom might have already been destroyed.
     215 *
     216 * @param _id id of atom to remove
     217 */
     218void GLWorldScene::atomRemoved(const atomicNumber_t _id)
     219{
     220  LOG(3, "INFO: GLWorldScene: Received signal atomRemoved for atom "+toString(_id)+".");
     221  // bonds are removed by signal coming from ~bond
     222  // remove atoms
     223  AtomNodeMap::iterator iter = AtomsinSceneMap.find(_id);
     224  ASSERT(iter != AtomsinSceneMap.end(),
     225      "GLWorldScene::atomRemoved() - atom "+toString(_id)+" not on display.");
     226  GLMoleculeObject_atom *atomObject = iter->second;
     227  atomObject->disconnect();
     228  AtomsinSceneMap.erase(iter);
     229  delete atomObject;
     230  emit changeOccured();
     231}
     232
     233/** ....
     234 *
     235 */
     236void GLWorldScene::worldSelectionChanged()
     237{
     238  LOG(3, "INFO: GLWorldScene: Received signal selectionChanged.");
     239
     240  const std::vector<molecule*> &molecules = World::getInstance().getAllMolecules();
     241
     242  if (molecules.size() > 0) {
     243    for (std::vector<molecule*>::const_iterator Runner = molecules.begin();
     244        Runner != molecules.end();
     245        Runner++) {
     246
     247      MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find((*Runner)->getId());
     248      bool isSelected = World::getInstance().isSelected(*Runner);
     249
     250      // molecule selected but not in scene?
     251      if (isSelected && (iter == MoleculesinSceneMap.end())){
     252        // -> create new mesh
     253        GLMoleculeObject_molecule *molObject = new GLMoleculeObject_molecule(meshEmpty, this, *Runner);
     254        MoleculesinSceneMap.insert( make_pair((*Runner)->getId(), molObject) );
     255        connect (molObject, SIGNAL(changed()), this, SIGNAL(changed()));
     256        connect (molObject, SIGNAL(selectionChanged()), this, SIGNAL(changed()));
     257        connect (molObject, SIGNAL(selectionChanged()), this, SIGNAL(changed()));
     258        emit changed();
     259        emit changeOccured();
     260      }
     261
     262      // molecule not selected but in scene?
     263      if (!isSelected && (iter != MoleculesinSceneMap.end())){
     264        // -> remove from scene
     265        moleculeRemoved(*Runner);
     266      }
     267
     268    }
     269  }
     270}
     271
     272/** Removes a molecule from the scene.
     273 *
     274 * @param _molecule molecule to remove
     275 */
     276void GLWorldScene::moleculeRemoved(const molecule *_molecule)
     277{
     278  LOG(3, "INFO: GLWorldScene: Received signal moleculeRemoved for molecule "+toString(_molecule->getId())+".");
     279  MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_molecule->getId());
     280
     281  // only remove if the molecule is in the scene
     282  //  (= is selected)
     283  if (iter != MoleculesinSceneMap.end()){
     284    GLMoleculeObject_molecule *molObject = iter->second;
     285    molObject->disconnect();
     286    MoleculesinSceneMap.erase(iter);
     287    delete molObject;
     288    emit changed();
     289    emit changeOccured();
     290  }
     291}
     292
     293/** Helper function to get bond ids in the correct order for BondNodeMap.
     294 *
     295 * \return pair of ids in correct order.
     296 */
     297GLWorldScene::BondIds GLWorldScene::getBondIds(
     298    const bond::ptr _bond,
     299    const enum GLMoleculeObject_bond::SideOfBond _side) const
     300{
     301  BondIds ids;
     302  switch (_side) {
     303    case GLMoleculeObject_bond::left:
     304      ids = std::make_pair(_bond->leftatom->getId(), _bond->rightatom->getId());
     305      break;
     306    case GLMoleculeObject_bond::right:
     307      ids = std::make_pair(_bond->rightatom->getId(), _bond->leftatom->getId());
     308      break;
     309  }
     310  return ids;
     311}
     312
     313/** Adds a bond to the scene.
     314 *
     315 * @param _bond bond to add
     316 * @param side which side of the bond (left or right)
     317 */
     318void GLWorldScene::bondInserted(const bond::ptr _bond, const enum GLMoleculeObject_bond::SideOfBond _side)
     319{
     320  LOG(3, "INFO: GLWorldScene::bondInserted() - Adding bond "+toString(*_bond)+".");
     321  //LOG(4, "INFO: Currently present bonds " << BondsinSceneMap << ".");
     322
     323  const BondIds ids = getBondIds(_bond, _side);
     324  BondNodeMap::iterator iter = BondsinSceneMap.find(ids);
     325  if (iter == BondsinSceneMap.end()) {
     326    GLMoleculeObject_bond * bondObject =
     327        new GLMoleculeObject_bond(meshCylinder, this, _bond, _side);
     328    connect (
     329        bondObject, SIGNAL(BondRemoved(const atomId_t, const atomId_t)),
     330        this, SLOT(bondRemoved(const atomId_t, const atomId_t)));
     331    connect (bondObject, SIGNAL(changed()), this, SIGNAL(changed()));
     332    BondsinSceneMap.insert( make_pair(ids, bondObject) );
     333  //    BondIdsinSceneMap.insert( Leftids );
     334  } else {
     335    iter->second->resetPosition();
     336    iter->second->resetWidth();
     337  }
     338  emit changeOccured();
     339}
     340
     341/** Removes a bond from the scene.
     342 *
     343 * @param _bond bond to remove
     344 */
     345void GLWorldScene::bondRemoved(const atomId_t leftnr, const atomId_t rightnr)
     346{
     347  LOG(3, "INFO: GLWorldScene::bondRemoved() - Removing bond between "+toString(leftnr)+" and "+toString(rightnr)+".");
     348  {
     349    // left bond
     350    const BondIds Leftids( make_pair(leftnr, rightnr) );
     351    BondNodeMap::iterator leftiter = BondsinSceneMap.find( Leftids );
     352    ASSERT(leftiter != BondsinSceneMap.end(),
     353        "GLWorldScene::bondRemoved() - bond "+toString(leftnr)+"-"
     354        +toString(rightnr)+" not on display.");
     355    GLMoleculeObject_bond *bondObject = leftiter->second;
     356    BondsinSceneMap.erase(leftiter);
     357    delete bondObject; // is done by signal from bond itself
     358    //LOG(4, "INFO: Still present bonds " << BondsinSceneMap << ".");
     359  }
     360
     361  emit changeOccured();
     362}
     363
     364/** Adds a shape to the scene.
     365 *
     366 * uses ShapeRegistry::lastChanged()
     367 *
     368 */
     369void GLWorldScene::addShape()
     370{
     371  Shape &shape = *ShapeRegistry::getInstance().lastChanged();
     372  GLMoleculeObject_shape *shapeObject = new GLMoleculeObject_shape(shape, this);
     373  ShapeNodeMap::iterator iter = ShapesinSceneMap.find(shape.getName());
     374  ASSERT(iter == ShapesinSceneMap.end(),
     375      "GLWorldScene::addShape() - same shape "+shape.getName()+" added again.");
     376  ShapesinSceneMap.insert( make_pair(shape.getName(), shapeObject) );
     377}
     378
     379void GLWorldScene::removeShape()
     380{
     381  Shape &shape = *ShapeRegistry::getInstance().lastChanged();
     382  ShapeNodeMap::iterator iter = ShapesinSceneMap.find(shape.getName());
     383  ASSERT(iter != ShapesinSceneMap.end(),
     384      "GLWorldScene::removeShape() - shape "+shape.getName()+" not in scene.");
     385  ShapesinSceneMap.erase(iter);
     386  delete(iter->second);
     387}
     388
     389void GLWorldScene::updateSelectedShapes()
     390{
     391  foreach (QObject *obj, children()) {
     392    GLMoleculeObject_shape *shapeobj = qobject_cast<GLMoleculeObject_shape *>(obj);
     393      if (shapeobj){
     394        shapeobj->enable(ShapeRegistry::getInstance().isSelected(shapeobj->getShape()));
     395      }
     396  }
     397}
     398
     399void GLWorldScene::initialize(QGLView *view, QGLPainter *painter) const
     400{
     401  // Initialize all of the mesh objects that we have as children.
     402   foreach (QObject *obj, children()) {
     403     GLMoleculeObject *meshobj = qobject_cast<GLMoleculeObject *>(obj);
     404       if (meshobj)
     405         meshobj->initialize(view, painter);
     406   }
     407}
     408
     409void GLWorldScene::draw(QGLPainter *painter, const QVector4D &cameraPlane) const
     410{
     411   // Draw all of the mesh objects that we have as children.
     412   foreach (QObject *obj, children()) {
     413     GLMoleculeObject *meshobj = qobject_cast<GLMoleculeObject *>(obj);
     414       if (meshobj)
     415         meshobj->draw(painter, cameraPlane);
     416   }
    138417}
    139418
    140419void GLWorldScene::atomClicked(atomId_t no)
    141420{
    142    LOG(3, "INFO: GLMoleculeObject_molecule - atom " << no << " has been clicked.");
     421   LOG(3, "INFO: GLWorldScene - atom " << no << " has been clicked.");
    143422   const atom *Walker = World::getInstance().getAtom(AtomById(no));
    144423   if (selectionMode == SelectAtom){
    … …  
    150429     const molecule *mol = Walker->getMolecule();
    151430     ASSERT(mol, "Atom without molecule has been clicked.");
    152      molids_t ids(1, mol->getId());
    153431     if (!World::getInstance().isSelected(mol))
    154        SelectionMoleculeById(ids);
     432       SelectionMoleculeById(mol->getId());
    155433     else
    156        SelectionNotMoleculeById(ids);
     434       SelectionNotMoleculeById(mol->getId());
    157435   }
    158436   emit clicked(no);
    159437}
    160438
    161 void GLWorldScene::moleculeClicked(moleculeId_t no)
    162 {
    163    LOG(3, "INFO: GLMoleculeObject_molecule - mol " << no << " has been clicked.");
    164    const molecule *mol= World::getInstance().getMolecule(MoleculeById(no));
    165    ASSERT(mol, "Atom without molecule has been clicked.");
    166    molids_t ids(1, mol->getId());
    167    if (!World::getInstance().isSelected(mol))
    168      SelectionMoleculeById(ids);
    169    else
    170      SelectionNotMoleculeById(ids);
    171    emit clicked(no);
    172 }
    173 
    174 
    175 /** Adds an atom to the scene.
    176  *
    177  * @param _atom atom to add
    178  */
    179 void GLWorldScene::atomInserted(const atomId_t _id)
    180 {
    181   LOG(3, "INFO: GLWorldScene: Received signal atomInserted for atom "+toString(_id)+".");
    182   // find associated molecule
    183   const moleculeId_t molid = World::getInstance().getAtom(AtomById(_id))->getMolecule()->getId();
    184   MoleculeNodeMap::const_iterator moliter = MoleculesinSceneMap.find(molid );
    185   ASSERT(moliter != MoleculesinSceneMap.end(),
    186       "GLWorldScene::atomAdded() - molecule with id of "+toString(molid)
    187       +" atom with id "+toString(_id)+" is unknown.");
    188   GLMoleculeObject_molecule *molObject = moliter->second;
    189 
    190   // add atom to internal list
    191 #ifndef NDEBUG
    192   AtomMoleculeMap::const_iterator atomiter = AtomsinSceneMap.find(_id);
    193     ASSERT(atomiter == AtomsinSceneMap.end(),
    194         "GLWorldScene::atomRemoved() - atom "+toString(_id)+" already known.");
    195 #endif
    196   AtomsinSceneMap.insert( std::make_pair( _id, molObject ));
    197 
    198   // inform its GlMoleculeObject_molecule.
    199   molObject->atomInserted(_id);
    200 
    201   // emit change
    202   emit changeOccured();
    203 }
    204 
    205 /** Removes an atom from the scene.
    206  *
    207  * We just the id as the atom might have already been destroyed.
    208  *
    209  * @param _id id of atom to remove
    210  */
    211 void GLWorldScene::atomRemoved(const atomId_t _id)
    212 {
    213   LOG(3, "INFO: GLWorldScene: Received signal atomRemoved for atom "+toString(_id)+".");
    214   // find associated molecule
    215   AtomMoleculeMap::iterator iter = AtomsinSceneMap.find(_id);
    216   ASSERT(iter != AtomsinSceneMap.end(),
    217       "GLWorldScene::atomRemoved() - atom "+toString(_id)+" not on display.");
    218   GLMoleculeObject_molecule *molObject = iter->second;
    219 
    220   // remove from internal list
    221   AtomsinSceneMap.erase(iter);
    222 
    223   // inform its GlMoleculeObject_molecule.
    224   molObject->atomRemoved(_id);
    225 
    226   // emit change
    227   emit changeOccured();
    228 }
    229 
    230 /** ....
    231  *
    232  */
    233 void GLWorldScene::worldSelectionChanged()
    234 {
    235   LOG(3, "INFO: GLWorldScene: Received signal selectionChanged.");
    236 
    237   const std::vector<molecule*> &molecules = World::getInstance().getAllMolecules();
    238 
    239   if (molecules.size() > 0) {
    240     for (std::vector<molecule*>::const_iterator Runner = molecules.begin();
    241         Runner != molecules.end();
    242         Runner++) {
    243 
    244       // molecule selected but not in scene?
    245       const bool isSelected = World::getInstance().isSelected(*Runner);
    246       if (isSelected){
    247         MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find((*Runner)->getId());
    248         ASSERT( iter != MoleculesinSceneMap.end(),
    249             "GLWorldScene::worldSelectionChanged() - selected molecule is unknown.");
    250         GLMoleculeObject_molecule *molObject = iter->second;
    251         // inform molecule object
    252         molObject->selected(isSelected);
    253       }
    254     }
    255   }
    256 }
    257 
    258 /** Inserts a molecule into the scene.
    259  *
    260  * @param _mol molecule to insert
    261  */
    262 void GLWorldScene::moleculeInserted(const molecule * _mol)
    263 {
    264   LOG(3, "INFO: GLWorldScene: Received signal moleculeRemoved for molecule "+toString(_mol->getId())+".");
    265   MoleculeNodeMap::const_iterator iter = MoleculesinSceneMap.find(_mol->getId());
    266   ASSERT( iter == MoleculesinSceneMap.end(),
    267       "GLWorldScene::moleculeInserted() - molecule's id "+toString(_mol->getId())+" already present.");
    268 
    269   // add new object
    270   GLMoleculeObject_molecule *molObject = new GLMoleculeObject_molecule(GLMoleculeObject::meshEmpty, this, _mol);
    271   MoleculesinSceneMap.insert( make_pair(_mol->getId(), molObject) );
    272   connect (molObject, SIGNAL(changed()), this, SIGNAL(changed()));
    273   connect (molObject, SIGNAL(changeOccured()), this, SIGNAL(changeOccured()));
    274   connect (molObject, SIGNAL(atomClicked(atomId_t)), this, SLOT(atomClicked(atomId_t)));
    275   connect (molObject, SIGNAL(moleculeClicked(moleculeId_t)), this, SLOT(moleculeClicked(moleculeId_t)));
    276   connect (molObject, SIGNAL(changeAtomId(GLMoleculeObject_atom *, int, int)), this, SLOT(changeAtomId(GLMoleculeObject_atom *, int, int)));
    277   connect (molObject, SIGNAL(selectionChanged()), this, SIGNAL(changed()));
    278   connect (molObject, SIGNAL(selectionChanged()), this, SIGNAL(changed()));
    279   connect (molObject, SIGNAL(hoverChanged(const atom &)), this, SIGNAL(hoverChanged(const atom &)));
    280   connect (molObject, SIGNAL(hoverChanged(const molecule &, int)), this, SIGNAL(hoverChanged(const molecule &, int)));
    281   emit changed();
    282   emit changeOccured();
    283 }
    284 
    285 /** Removes a molecule from the scene.
    286  *
    287  * @param _id id of molecule to remove
    288  */
    289 void GLWorldScene::moleculeRemoved(const moleculeId_t _id)
    290 {
    291   LOG(3, "INFO: GLWorldScene: Received signal moleculeRemoved for molecule "+toString(_id)+".");
    292   MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_id);
    293   ASSERT( iter != MoleculesinSceneMap.end(),
    294       "GLWorldScene::moleculeInserted() - molecule's id "+toString(_id)+" is unknown.");
    295 
    296   GLMoleculeObject_molecule *molObject = iter->second;
    297   molObject->disconnect();
    298   MoleculesinSceneMap.erase(iter);
    299   delete molObject;
    300   emit changed();
    301   emit changeOccured();
    302 }
    303 
    304 void GLWorldScene::moleculesVisibilityChanged(const moleculeId_t _id, bool _visible)
    305 {
    306   MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_id);
    307   ASSERT( iter != MoleculesinSceneMap.end(),
    308       "GLWorldScene::moleculeInserted() - molecule's id "+toString(_id)+" is unknown.");
    309 
    310   GLMoleculeObject_molecule *molObject = iter->second;
    311   molObject->setVisible(_visible);
    312 
    313   emit changed();
    314   emit changeOccured();
    315 }
    316 
    317 /** Adds a bond to the scene.
    318  *
    319  * @param _bond bond to add
    320  * @param side which side of the bond (left or right)
    321  */
    322 void GLWorldScene::bondInserted(const bond::ptr _bond, const enum GLMoleculeObject_bond::SideOfBond _side)
    323 {
    324   LOG(3, "INFO: GLWorldScene::bondInserted() - Adding bond "+toString(*_bond)+".");
    325   //LOG(4, "INFO: Currently present bonds " << BondsinSceneMap << ".");
    326   // bond partners must both belong to same atom
    327   ASSERT( _bond->leftatom->getMolecule() == _bond->rightatom->getMolecule(),
    328       "GLWorldScene::bondInserted() - bond partners do not belong to same molecule.");
    329 
    330   // find associated molecule object
    331   const moleculeId_t molid = _bond->leftatom->getMolecule()->getId();
    332   MoleculeNodeMap::const_iterator moliter = MoleculesinSceneMap.find(molid );
    333   ASSERT(moliter != MoleculesinSceneMap.end(),
    334       "GLWorldScene::bondInserted() - molecule with id of "+toString(molid)
    335       +" atom with id "+toString(_bond->leftatom->getId())+" is unknown.");
    336   GLMoleculeObject_molecule *molObject = moliter->second;
    337 
    338   // add to internal list
    339   const GLMoleculeObject_molecule::BondIds ids =
    340       GLMoleculeObject_molecule::getBondIds(_bond, _side);
    341   BondMoleculeMap::const_iterator iter = BondsinSceneMap.find(ids);
    342   ASSERT(iter == BondsinSceneMap.end(),
    343       "GLWorldScene::bondInserted() - bond with ids "+toString(ids.first)
    344       +","+toString(ids.second)+" already present.");
    345   BondsinSceneMap.insert( std::make_pair( ids, molObject ));
    346 
    347   // inform its GlMoleculeObject_molecule.
    348   molObject->bondInserted(_bond, _side);
    349 
    350   // emit change
    351   emit changeOccured();
    352 }
    353 
    354 /** Removes a bond from the scene.
    355  *
    356  * @param _bond bond to remove
    357  */
    358 void GLWorldScene::bondRemoved(const atomId_t leftnr, const atomId_t rightnr)
    359 {
    360   LOG(3, "INFO: GLWorldScene::bondRemoved() - Removing bond between "+toString(leftnr)+" and "+toString(rightnr)+".");
    361   {
    362     // left bond
    363     const GLMoleculeObject_molecule::BondIds Leftids( make_pair(leftnr, rightnr) );
    364     BondMoleculeMap::iterator leftiter = BondsinSceneMap.find( Leftids );
    365     ASSERT(leftiter != BondsinSceneMap.end(),
    366         "GLWorldScene::bondRemoved() - bond "+toString(leftnr)+"-"
    367         +toString(rightnr)+" not on display.");
    368     GLMoleculeObject_molecule *molObject = leftiter->second;
    369 
    370     // remove from internal list
    371     BondsinSceneMap.erase(leftiter);
    372 
    373     // inform its GlMoleculeObject_molecule.
    374     molObject->bondRemoved( leftnr, rightnr );
    375   }
    376 
    377   // emit change
    378   emit changeOccured();
    379 }
    380 
    381 /** Adds a shape to the scene.
    382  *
    383  * uses ShapeRegistry::lastChanged()
    384  *
    385  */
    386 void GLWorldScene::addShape()
    387 {
    388   Shape &shape = *ShapeRegistry::getInstance().lastChanged();
    389   GLMoleculeObject_shape *shapeObject = new GLMoleculeObject_shape(shape, this);
    390   ShapeNodeMap::iterator iter = ShapesinSceneMap.find(shape.getName());
    391   ASSERT(iter == ShapesinSceneMap.end(),
    392       "GLWorldScene::addShape() - same shape "+shape.getName()+" added again.");
    393   ShapesinSceneMap.insert( make_pair(shape.getName(), shapeObject) );
    394 }
    395 
    396 void GLWorldScene::removeShape()
    397 {
    398   Shape &shape = *ShapeRegistry::getInstance().lastChanged();
    399   ShapeNodeMap::iterator iter = ShapesinSceneMap.find(shape.getName());
    400   ASSERT(iter != ShapesinSceneMap.end(),
    401       "GLWorldScene::removeShape() - shape "+shape.getName()+" not in scene.");
    402   ShapesinSceneMap.erase(iter);
    403   delete(iter->second);
    404 }
    405 
    406 void GLWorldScene::updateSelectedShapes()
    407 {
    408   foreach (QObject *obj, children()) {
    409     GLMoleculeObject_shape *shapeobj = qobject_cast<GLMoleculeObject_shape *>(obj);
    410       if (shapeobj){
    411         shapeobj->enable(ShapeRegistry::getInstance().isSelected(shapeobj->getShape()));
    412       }
    413   }
    414 }
    415 
    416 void GLWorldScene::initialize(QGLView *view, QGLPainter *painter) const
    417 {
    418   // Initialize all of the mesh objects that we have as children.
    419    foreach (QObject *obj, children()) {
    420      GLMoleculeObject *meshobj = qobject_cast<GLMoleculeObject *>(obj);
    421        if (meshobj)
    422          meshobj->initialize(view, painter);
    423    }
    424 }
    425 
    426 void GLWorldScene::draw(QGLPainter *painter, const QVector4D &cameraPlane) const
    427 {
    428    // Draw all of the mesh objects that we have as children.
    429    foreach (QObject *obj, children()) {
    430      GLMoleculeObject *meshobj = qobject_cast<GLMoleculeObject *>(obj);
    431        if (meshobj)
    432          meshobj->draw(painter, cameraPlane);
    433    }
    434 }
    435 
    436439void GLWorldScene::setSelectionMode(SelectionModeType mode)
    437440{
    … …  
    450453}
    451454
     455void GLWorldScene::hoverChangedSignalled(GLMoleculeObject *ob)
     456{
     457  // Find the atom, ob corresponds to.
     458  hoverAtom = NULL;
     459  GLMoleculeObject_atom *atomObject = dynamic_cast<GLMoleculeObject_atom *>(ob);
     460  if (atomObject){
     461    for (AtomNodeMap::iterator iter = AtomsinSceneMap.begin();iter != AtomsinSceneMap.end(); ++ iter){
     462      if (iter->second == atomObject)
     463        hoverAtom = World::getInstance().getAtom(AtomById(iter->first));
     464    }
     465  }
     466
     467  // Propagate signal.
     468  emit hoverChanged(hoverAtom);
     469}
     470
    452471void GLWorldScene::changeAtomId(GLMoleculeObject_atom *ob, int oldId, int newId)
    453472{
    454473  LOG(3, "INFO: GLWorldScene - change atom id " << oldId << " to " << newId << ".");
    455474  // Remove from map.
    456   AtomMoleculeMap::iterator iter = AtomsinSceneMap.find(oldId);
     475  AtomNodeMap::iterator iter = AtomsinSceneMap.find(oldId);
    457476  ASSERT(iter != AtomsinSceneMap.end(),
    458         "GLWorldScene::changeAtomId() - atom with old id "+toString(oldId)+" not on display.");
    459   GLMoleculeObject_molecule *molObject = iter->second;
    460 
    461   // erase by signalling removal
    462   molObject->atomRemoved(oldId);
    463 
    464   // remove from internal list
     477        "GLWorldScene::objectIdChangedSignalled() - atom with id "+toString(oldId)+" not on display.");
     478  GLMoleculeObject_atom *atomObject = iter->second;
    465479  AtomsinSceneMap.erase(iter);
    466480
    467481  // Reinsert with new id.
    468   {
    469     AtomMoleculeMap::iterator iter = AtomsinSceneMap.find(newId);
    470     ASSERT(iter == AtomsinSceneMap.end(),
    471           "GLWorldScene::changeAtomId() - atom with new id "+toString(newId)+" already known.");
    472   }
    473   AtomsinSceneMap.insert( make_pair(newId, molObject) );
    474 
    475   // inform molecule object
    476   molObject->atomInserted(oldId);
    477 }
     482  AtomsinSceneMap.insert( make_pair(newId, atomObject) );
     483}
     484

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

    r0ac85c3 r7b38d3  
    7575  void clicked(atomId_t);
    7676  void doubleClicked();
    77   void hoverChanged(const atom &);
    78   void hoverChanged(const molecule &, int);
     77  void hoverChanged(const atom*);
    7978
    8079private slots:
    8180  void atomClicked(atomId_t no);
    82   void atomInserted(const atomId_t _id);
    83   void atomRemoved(const atomId_t _id);
    84   void moleculeClicked(moleculeId_t no);
    85   void moleculeRemoved(const moleculeId_t _id);
    86   void moleculeInserted(const molecule * _mol);
     81  void atomInserted(const atomicNumber_t _id);
     82  void atomRemoved(const atomicNumber_t _id);
     83  void moleculeRemoved(const molecule *_molecule);
    8784  void worldSelectionChanged();
    8885  void bondInserted(const bond::ptr _bond, const GLMoleculeObject_bond::SideOfBond side);
    … …  
    9087  void setSelectionModeAtom();
    9188  void setSelectionModeMolecule();
     89  void hoverChangedSignalled(GLMoleculeObject *ob);
    9290  void changeAtomId(GLMoleculeObject_atom *ob, int oldId, int newOd);
    9391  void addShape();
    9492  void removeShape();
    9593  void update();
    96   void moleculesVisibilityChanged(const moleculeId_t _id, bool _visible);
    9794
    9895public:
    … …  
    103100
    104101private:
     102  typedef std::pair< atomId_t, atomId_t> BondIds;
     103  friend std::ostream &operator<<(std::ostream &ost, const BondIds &t);
    105104
    106   typedef std::map< atomId_t, GLMoleculeObject_molecule* > AtomMoleculeMap;
    107   typedef std::map< GLMoleculeObject_molecule::BondIds , GLMoleculeObject_molecule* > BondMoleculeMap;
     105  BondIds getBondIds(
     106      const bond::ptr _bond,
     107      const enum GLMoleculeObject_bond::SideOfBond side) const;
     108
     109  typedef std::map< atomId_t, GLMoleculeObject_atom* > AtomNodeMap;
     110  typedef std::map< BondIds , GLMoleculeObject_bond* > BondNodeMap;
    108111  typedef std::map< moleculeId_t , GLMoleculeObject_molecule* > MoleculeNodeMap;
    109112  typedef std::map< std::string , GLMoleculeObject_shape* > ShapeNodeMap;
    110   AtomMoleculeMap AtomsinSceneMap;
    111   BondMoleculeMap BondsinSceneMap;
     113  AtomNodeMap AtomsinSceneMap;
     114  BondNodeMap BondsinSceneMap;
    112115  MoleculeNodeMap MoleculesinSceneMap;
    113116  ShapeNodeMap ShapesinSceneMap;
    114117
     118  QGLSceneNode *meshEmpty[GLMoleculeObject::DETAILTYPES_MAX];
     119  QGLSceneNode *meshSphere[GLMoleculeObject::DETAILTYPES_MAX];
     120  QGLSceneNode *meshCylinder[GLMoleculeObject::DETAILTYPES_MAX];
     121
    115122  SelectionModeType selectionMode;
     123  const atom *hoverAtom;
    116124};
    117125
     126std::ostream &operator<<(std::ostream &ost, const GLWorldScene::BondIds &t);
     127
    118128#endif /* GLWORLDSCENE_HPP_ */

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

    r0ac85c3 r7b38d3  
    7171  setOption(QGLView::ObjectPicking, true);
    7272  setOption(QGLView::CameraNavigation, false);
    73   setFocusPolicy(Qt::StrongFocus);
    7473  setCameraControlMode(Rotate);
    7574  defaultEyeSeparation = 4.0;
    … …  
    7978  //changeMaterials(false);
    8079
    81   qRegisterMetaType<atomId_t>("atomId_t");
    82   qRegisterMetaType<moleculeId_t>("moleculeId_t");
     80  qRegisterMetaType<atomicNumber_t>("atomicNumber_t");
    8381
    8482  connect(this, SIGNAL(ShapeAdded()), worldscene, SLOT(addShape()));
    … …  
    8785  connect(worldscene, SIGNAL(changeOccured()), this, SLOT(changeSignalled()));
    8886  connect(worldscene, SIGNAL(changed()), this, SIGNAL(changed()));
    89   connect(worldscene, SIGNAL(hoverChanged(const atom &)), this, SLOT(sceneHoverSignalled(const atom &)));
    90   connect(worldscene, SIGNAL(hoverChanged(const molecule &, int)), this, SLOT(sceneHoverSignalled(const molecule &, int)));
     87  connect(worldscene, SIGNAL(hoverChanged(const atom *)), this, SLOT(sceneHoverSignalled(const atom *)));
     88  connect(this, SIGNAL(atomInserted(const atomicNumber_t)), worldscene, SLOT(atomInserted(const atomicNumber_t)));
     89  connect(this, SIGNAL(atomRemoved(const atomicNumber_t)), worldscene, SLOT(atomRemoved(const atomicNumber_t)));
    9190  connect(this, SIGNAL(worldSelectionChanged()), worldscene, SLOT(worldSelectionChanged()));
    92   connect(this, SIGNAL(moleculeRemoved(const moleculeId_t)), worldscene, SLOT(moleculeRemoved(const moleculeId_t)));
    93   connect(this, SIGNAL(moleculeInserted(const molecule *)), worldscene, SLOT(moleculeInserted(const molecule *)));
     91  connect(this, SIGNAL(moleculeRemoved(const molecule *)), worldscene, SLOT(moleculeRemoved(const molecule *)));
     92  //connect(this, SIGNAL(moleculeInserted(const molecule *)), worldscene, SLOT(moleculeInserted(const molecule *)));
    9493  //connect(this, SIGNAL(changed()), this, SLOT(updateGL()));
    9594  connect(this, SIGNAL(changed()), this, SLOT(sceneChangeSignalled()));
    96   connect(this, SIGNAL(moleculesVisibilityChanged(const moleculeId_t,bool)), worldscene, SLOT(moleculesVisibilityChanged(const moleculeId_t,bool)));
    9795
    9896  // sign on to changes in the world
    9997  World::getInstance().signOn(this);
     98  World::getInstance().signOn(this, World::AtomInserted);
     99  World::getInstance().signOn(this, World::AtomRemoved);
    100100  World::getInstance().signOn(this, World::MoleculeInserted);
    101101  World::getInstance().signOn(this, World::MoleculeRemoved);
    … …  
    338338  if (static_cast<World *>(publisher) == World::getPointer()) {
    339339    switch (notification->getChannelNo()) {
     340      case World::AtomInserted:
     341      {
     342        const atomicNumber_t _id = World::getInstance().lastChanged<atom>()->getId();
     343  #ifdef LOG_OBSERVER
     344        observerLog().addMessage() << "++ Observer " << observerLog().getName(static_cast<Observer *>(this)) << " received notification that atom "+toString(_id)+" has been inserted.";
     345  #endif
     346        emit atomInserted(_id);
     347        break;
     348      }
     349      case World::AtomRemoved:
     350      {
     351        const atomicNumber_t _id = World::getInstance().lastChanged<atom>()->getId();
     352  #ifdef LOG_OBSERVER
     353        observerLog().addMessage() << "++ Observer " << observerLog().getName(static_cast<Observer *>(this)) << " received notification that atom "+toString(_id)+" has been removed.";
     354  #endif
     355        emit atomRemoved(_id);
     356        break;
     357      }
    340358      case World::SelectionChanged:
    341359      {
    … …  
    348366      case World::MoleculeInserted:
    349367      {
    350         const molecule * _mol = World::getInstance().lastChanged<molecule>();
     368        const molecule *_molecule = World::getInstance().lastChanged<molecule>();
    351369  #ifdef LOG_OBSERVER
    352         observerLog().addMessage() << "++ Observer " << observerLog().getName(static_cast<Observer *>(this)) << " received notification that molecule "+toString(_mol->getId())+" has been removed.";
     370        observerLog().addMessage() << "++ Observer " << observerLog().getName(static_cast<Observer *>(this)) << " received notification that molecule "+toString(_molecule->getId())+" has been removed.";
    353371  #endif
    354         emit moleculeInserted(_mol);
     372        emit moleculeInserted(_molecule);
    355373        break;
    356374      }
    357375      case World::MoleculeRemoved:
    358376      {
    359         const moleculeId_t _id = World::getInstance().lastChanged<molecule>()->getId();
     377        const molecule *_molecule = World::getInstance().lastChanged<molecule>();
    360378  #ifdef LOG_OBSERVER
    361         observerLog().addMessage() << "++ Observer " << observerLog().getName(static_cast<Observer *>(this)) << " received notification that molecule "+toString(_id)+" has been removed.";
     379        observerLog().addMessage() << "++ Observer " << observerLog().getName(static_cast<Observer *>(this)) << " received notification that molecule "+toString(_molecule->getId())+" has been removed.";
    362380  #endif
    363         emit moleculeRemoved(_id);
     381        emit moleculeRemoved(_molecule);
    364382        break;
    365383      }
    … …  
    500518void GLWorldView::keyPressEvent(QKeyEvent *e)
    501519{
    502   // Find the distance between the eye and focus point.
    503   QVector3D d = camera()->eye() - camera()->center();
    504 //  LOG(1, "Distance vector eye and center is "
    505 //      << d.x() << "," << d.y() << "," << d.z());
    506   // scale the move unit by the eye <-> domain center distance
    507   const double key_move_unit = 0.04*(d.length()/50.);
    508 
    509520  if (e->key() == Qt::Key_Tab) {
    510521    // The Tab key turns the ShowPicking option on and off,
    … …  
    512523    setOption(QGLView::ShowPicking, ((options() & QGLView::ShowPicking) == 0));
    513524    updateGL();
    514   } else if ((e->key() == Qt::Key_Minus) || (e->key() == Qt::Key_Plus)) {
    515     // Scale the distance.
    516     if (e->key() == Qt::Key_Minus)
    517       d *= 1.2;
    518     else if (e->key() == Qt::Key_Plus)
    519       d /= 1.2;
    520     // Set new eye position.
    521     camera()->setEye(camera()->center() + d);
    522   } else if ((e->key() == Qt::Key_Left) || (e->key() == Qt::Key_Right)) {
    523     // Translate the camera.
    524     const double d = (e->key() == Qt::Key_Left) ? -key_move_unit : key_move_unit;
    525     camera()->translateCenter( d, 0., 0);
    526     camera()->translateEye( d, 0., 0);
    527   } else if ((e->key() == Qt::Key_Up) || (e->key() == Qt::Key_Down)) {
    528     // Translate the camera.
    529     const double d = (e->key() == Qt::Key_Up) ? -key_move_unit : key_move_unit;
    530     camera()->translateCenter( 0., d, 0);
    531     camera()->translateEye( 0., d, 0);
    532   } else if ((e->key() == Qt::Key_PageUp) || (e->key() == Qt::Key_PageDown)) {
    533     // Translate the camera.
    534     const double d = (e->key() == Qt::Key_PageUp) ? -key_move_unit : key_move_unit;
    535     camera()->translateCenter( 0., 0., d);
    536     camera()->translateEye( 0., 0., d);
    537525  }
    538526  QGLView::keyPressEvent(e);
    … …  
    762750}
    763751
    764 void GLWorldView::sceneHoverSignalled(const atom &_atom)
     752void GLWorldView::sceneHoverSignalled(const atom *_atom)
    765753{
    766754  emit hoverChanged(_atom);
    767755}
    768 
    769 void GLWorldView::sceneHoverSignalled(const molecule &_mol, int _i)
    770 {
    771   emit hoverChanged(_mol, _i);
    772 }

  • src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp

    r0ac85c3 r7b38d3  
    5151  void checkChanges();
    5252  void sceneChangeSignalled();
    53   void sceneHoverSignalled(const atom &_atom);
    54   void sceneHoverSignalled(const molecule &_mol, int);
     53  void sceneHoverSignalled(const atom *_atom);
    5554  void changeDreiBein();
    5655  void changeDomain();
    … …  
    5958  void changed();
    6059  void TimeChanged();
    61   void moleculeInserted(const molecule * _mol);
    62   void moleculeRemoved(const moleculeId_t _id);
     60  void atomInserted(const atomicNumber_t _id);
     61  void atomRemoved(const atomicNumber_t _id);
     62  void moleculeInserted(const molecule *_molecule);
     63  void moleculeRemoved(const molecule *_molecule);
    6364  void worldSelectionChanged();
    64   void hoverChanged(const atom &_atom);
    65   void hoverChanged(const molecule &_mol, int);
     65  void hoverChanged(const atom *_atom);
    6666  void ShapeAdded();
    6767  void ShapeRemoved();
    68   void moleculesVisibilityChanged(const moleculeId_t,bool);
    6968
    7069protected:

  • src/UIElements/Views/Qt4/QtInfoBox.cpp

    r0ac85c3 r7b38d3  
    5050    QTabWidget(),
    5151    curAtom(NULL), nextAtom(NULL),
    52     curMolecule(NULL), nextMolecule(NULL),
    5352    page_mol(NULL), page_atom(NULL)
    5453{
    … …  
    6867}
    6968
    70 void QtInfoBox::atomHover(const atom &_atom)
    71 {
    72   nextAtom = &_atom;
    73   timer->start(500);
    74 }
    75 
    76 void QtInfoBox::moleculeHover(const molecule &_mol)
    77 {
    78   nextMolecule = &_mol;
     69void QtInfoBox::atomHover(const atom *_atom)
     70{
     71  nextAtom = _atom;
    7972  timer->start(500);
    8073}
    … …  
    8477  if (nextAtom)
    8578    showAtom(nextAtom);
    86   if (nextMolecule)
    87     showMolecule(nextMolecule);
    8879}
    8980
    … …  
    110101
    111102  curAtom = _atom;
    112   nextAtom = NULL;
    113   nextMolecule = NULL;
    114103
    115104  // Show new tabs.
    … …  
    127116        setCurrentIndex(currentPage);
    128117    }
    129   }
    130 }
    131 
    132 void QtInfoBox::showMolecule(const molecule *_mol)
    133 {
    134   currentPage = currentIndex();
    135 
    136   // Remove old tabs.
    137   clearTabs();
    138 
    139   curMolecule = _mol;
    140   nextAtom = NULL;
    141   nextMolecule = NULL;
    142 
    143   // Show new tabs.
    144   if (curMolecule){
    145     page_mol = new QtMoleculeInfoPage(curMolecule, this);
    146     addTab(page_mol, "Molecule");
    147     connect(page_mol, SIGNAL(moleculeKilled()), this, SLOT(clearTabs()));
    148 
    149     if (currentPage > 0)
    150       setCurrentIndex(currentPage);
    151118  }
    152119}

  • src/UIElements/Views/Qt4/QtInfoBox.hpp

    r0ac85c3 r7b38d3  
    3636
    3737  void showAtom(const atom *_atom);
    38   void showMolecule(const molecule *_mol);
    3938
    4039public slots:
    41   void atomHover(const atom &_atom);
    42   void moleculeHover(const molecule &_mol);
     40  void atomHover(const atom *_atom);
    4341  void timerTimeout();
    4442
    … …  
    4846  const atom *curAtom;
    4947  const atom *nextAtom;
    50   const molecule *curMolecule;
    51   const molecule *nextMolecule;
    5248  QtMoleculeInfoPage *page_mol;
    5349  QtAtomInfoPage *page_atom;

  • src/UIElements/Views/Qt4/QtMoleculeList.cpp

    r0ac85c3 r7b38d3  
    5555// these attributes are skipped so far
    5656const int QtMoleculeList::COLUMNCOUNT = COLUMNTYPES_MAX;
    57 const char *QtMoleculeList::COLUMNNAMES[QtMoleculeList::COLUMNCOUNT]={"Name","Visibility", "Atoms","Formula","Occurrence"/*,"Size"*/};
     57const char *QtMoleculeList::COLUMNNAMES[QtMoleculeList::COLUMNCOUNT]={"Name","Atoms","Formula","Occurrence"/*,"Size"*/};
    5858
    5959QtMoleculeList::QtMoleculeList(QWidget * _parent) :
    … …  
    6969  setHeaderLabels(header);
    7070
    71   World::getInstance().signOn(this, World::MoleculeInserted);
    72   World::getInstance().signOn(this, World::MoleculeRemoved);
     71  World::getInstance().signOn(this);//, World::MoleculeInserted);
     72  //World::getInstance().signOn(this, World::MoleculeRemoved);
    7373
    7474
    … …  
    7676  clearing = false;
    7777  selecting = false;
    78   ChangingChildrensVisibility = false;
    7978  refill();
    8079
    … …  
    8281  //connect(this,SIGNAL(cellChanged(int,int)),this,SLOT(moleculeChanged(int,int)));
    8382  connect(selectionModel(),SIGNAL(selectionChanged(QItemSelection, QItemSelection)),this,SLOT(rowsSelected(QItemSelection, QItemSelection)));
    84   connect(this, SIGNAL(itemChanged(QTreeWidgetItem*, int)), this, SLOT(visibilityChanged(QTreeWidgetItem*, int)));
     83
    8584}
    8685
    8786QtMoleculeList::~QtMoleculeList()
    8887{
    89   World::getInstance().signOff(this, World::MoleculeInserted);
    90   World::getInstance().signOff(this, World::MoleculeRemoved);
     88  World::getInstance().signOff(this);//, World::MoleculeInserted);
     89  //World::getInstance().signOff(this, World::MoleculeRemoved);
    9190}
    9291
    9392void QtMoleculeList::update(Observable *publisher) {
    94   ASSERT(0,
    95       "QtMoleculeList::update() - we did not sign up for any global updates.");
    96 }
    97 
    98 void QtMoleculeList::recieveNotification(Observable *publisher, Notification_ptr notification) {
    9993
    10094  if (selecting)
    … …  
    10296
    10397  dirty = true;
    104 }
    105 
     98
     99  // force an update from Qt...
     100  clearing = true;
     101  clear();
     102  clearing = false;
     103}
    106104
    107105void QtMoleculeList::refill() {
    … …  
    110108
    111109  clear();
    112   formula.clear();
    113   FormulaVisibilityCountMap.clear();
     110
     111  // list of (unique) formulas in the world
     112  std::vector<Formula> formula;
    114113
    115114  for (std::vector<molecule*>::const_iterator iter = molecules.begin();
    … …  
    119118    // find group if already in list
    120119    QTreeWidgetItem *groupItem = NULL;
    121     const std::string &molecule_formula = (*iter)->getFormula().toString();
    122     FormulaTreeItemMap_t::const_iterator formulaiter =
    123         formula.find(molecule_formula);
     120    for (unsigned int j=0;j<formula.size();j++)
     121      if ((*iter)->getFormula() == formula[j]){
     122        groupItem = topLevelItem(j);
     123        break;
     124      }
    124125
    125126    // new molecule type -> create new group
    126     if (formulaiter == formula.end()){
    127       // insert new formula entry into visibility
    128 #ifndef NDEBUG
    129       std::pair< FormulaVisibilityCountMap_t::iterator, bool> visibilityinserter =
    130 #endif
    131           FormulaVisibilityCountMap.insert(
    132               std::make_pair( molecule_formula, (unsigned int)0) );
    133       ASSERT( visibilityinserter.second,
    134           "QtMoleculeList::refill() - molecule with formula "
    135           +molecule_formula+" already in FormulaVisibilityCountMap.");
    136 
    137       // create item and place into Map with formula as key
     127    if (!groupItem){
     128      formula.push_back((*iter)->getFormula());
    138129      groupItem = new QTreeWidgetItem(this);
    139       formula.insert( std::make_pair(molecule_formula, groupItem) );
    140       // fill item
    141       groupItem->setText(NAME, QString("default"));
    142       groupItem->setFlags((groupItem->flags() | Qt::ItemIsUserCheckable) ^ Qt::ItemIsSelectable);
    143       groupItem->setCheckState(VISIBILITY, Qt::Unchecked);
    144       groupItem->setText(ATOMCOUNT, QString::number(0));
    145       groupItem->setText(FORMULA, QString(""));
    146       groupItem->setText(OCCURRENCE, "0");
     130      groupItem->setText(0, QString("default"));
     131      groupItem->setText(1, QString::number(0));
     132      groupItem->setText(2, QString(""));
     133      groupItem->setText(3, "0");
    147134      groupItem->setData(0, Qt::UserRole, QVariant(-1));
    148     } else {
    149       groupItem = formulaiter->second;
    150135    }
    151136
    152137    // add molecule
    153138    QTreeWidgetItem *molItem = new QTreeWidgetItem(groupItem);
    154     molItem->setText(NAME, QString((*iter)->getName().c_str()));
    155     molItem->setFlags(molItem->flags() | Qt::ItemIsUserCheckable | Qt::ItemIsSelectable);
    156     molItem->setCheckState(VISIBILITY, Qt::Unchecked);
    157     molItem->setText(ATOMCOUNT, QString::number((*iter)->getAtomCount()));
    158     molItem->setText(FORMULA, QString(molecule_formula.c_str()));
     139    molItem->setText(0, QString((*iter)->getName().c_str()));
     140    molItem->setText(1, QString::number((*iter)->getAtomCount()));
     141    molItem->setText(2, QString((*iter)->getFormula().toString().c_str()));
    159142    const int index = (*iter)->getId();
    160143    molItem->setData(0, Qt::UserRole, QVariant(index));
    161144    molItem->setSelected(World::getInstance().isSelected(*iter));
    162145
     146
    163147    // increase group occurrence
    164     int count = groupItem->text(OCCURRENCE).toInt() + 1;
    165     groupItem->setText(OCCURRENCE, QString::number(count));
     148    int count = groupItem->text(3).toInt() + 1;
     149    groupItem->setText(3, QString::number(count));
    166150  }
    167151  dirty = false;
    … …  
    177161
    178162void QtMoleculeList::subjectKilled(Observable *publisher) {
    179 }
    180 
    181 void QtMoleculeList::visibilityChanged(QTreeWidgetItem* item, int column)
    182 {
    183   if ((!clearing) && (!ChangingChildrensVisibility))
    184     if (column == VISIBILITY) {
    185       const moleculeId_t molid = item->data(0, Qt::UserRole).toInt();
    186       const bool visible = item->checkState(VISIBILITY);
    187       if (molid != (unsigned int)-1) { // molecule item
    188         const molecule * const _molecule =
    189             World::getInstance().getMolecule(MoleculeById(molid));
    190         ASSERT( _molecule != NULL,
    191             "QtMoleculeList::visibilityChanged() - molecule with id "
    192             +toString(molid)+" is not known to World.");
    193         const std::string &molecule_formula = _molecule->getFormula().toString();
    194         ASSERT( FormulaVisibilityCountMap.count(molecule_formula) != 0,
    195             "QtMoleculeList::visibilityChanged() - molecule with formula " +molecule_formula
    196             +" is not present in FormulaVisibilityCountMap.");
    197 
    198         // get parent
    199         QTreeWidgetItem *groupItem = item->parent();
    200         ASSERT( groupItem != NULL,
    201             "QtMoleculeList::visibilityChanged() - item with id "+toString(molid)
    202             +" has not parent?");
    203         // check whether we have to set the group item
    204 
    205         ChangingChildrensVisibility = true;
    206         if (visible) {
    207           ++(FormulaVisibilityCountMap[molecule_formula]);
    208           // compare with occurence/total number of molecules
    209           if (FormulaVisibilityCountMap[molecule_formula] ==
    210               (unsigned int)(groupItem->text(OCCURRENCE).toInt()))
    211             groupItem->setCheckState(VISIBILITY, Qt::Checked);
    212         } else {
    213           --(FormulaVisibilityCountMap[molecule_formula]);
    214           // none selected anymore?
    215           if (FormulaVisibilityCountMap[molecule_formula] == 0)
    216             groupItem->setCheckState(VISIBILITY, Qt::Unchecked);
    217         }
    218         ChangingChildrensVisibility = false;
    219 
    220         emit moleculesVisibilityChanged(molid, visible);
    221 
    222       } else { // group item
    223 
    224         // go through all children, but don't enter for groupItem once more
    225         ChangingChildrensVisibility = true;
    226         for (int i=0;i<item->childCount();++i) {
    227           QTreeWidgetItem *molItem = item->child(i);
    228           const moleculeId_t molid = molItem->data(0, Qt::UserRole).toInt();
    229           ASSERT( molid != (unsigned int)-1,
    230               "QtMoleculeList::visibilityChanged() - to child with index"
    231               +toString(i)+" there is no molecule?");
    232           molItem->setCheckState(VISIBILITY, visible ? Qt::Checked : Qt::Unchecked);
    233 
    234           // emit signal
    235           emit moleculesVisibilityChanged(molid, visible);
    236         }
    237         // set current number of visible children
    238         const std::string molecule_formula =
    239             item->text(FORMULA).toStdString();
    240         FormulaVisibilityCountMap[molecule_formula] =
    241             visible ? item->text(OCCURRENCE).toInt() : 0;
    242 
    243         ChangingChildrensVisibility = false;
    244       }
    245     }
    246163}
    247164
    … …  
    268185  // Select all molecules which belong to newly selected rows.
    269186  QModelIndex index;
    270   {
    271     QModelIndexList items = selected.indexes();
    272     molids_t ids;
    273     ids.reserve(items.size());
    274     foreach (index, items)
    275       if (index.column() == 0){
    276         int mol_id = model()->data(index, Qt::UserRole).toInt();
    277         if (mol_id < 0)
    278           continue;
    279         ids.push_back(mol_id);
    280         //std::cout << "select molecule" << std::endl;
    281       }
    282     MoleCuilder::SelectionMoleculeById(ids);
    283   }
     187  QModelIndexList items = selected.indexes();
     188  foreach (index, items)
     189    if (index.column() == 0){
     190      int mol_id = model()->data(index, Qt::UserRole).toInt();
     191      if (mol_id < 0)
     192        continue;
     193      //std::cout << "select molecule" << std::endl;
     194      MoleCuilder::SelectionMoleculeById(mol_id);
     195    }
    284196
    285197  // Unselect all molecules which belong to newly unselected rows.
    286   {
    287     QModelIndexList items = deselected.indexes();
    288     molids_t ids;
    289     ids.reserve(items.size());
    290     foreach (index, items)
    291       if (index.column() == 0){
    292         int mol_id = model()->data(index, Qt::UserRole).toInt();
    293         if (mol_id < 0)
    294           continue;
    295         //std::cout << "unselect molecule" << std::endl;
    296         ids.push_back(mol_id);
    297       }
    298     MoleCuilder::SelectionNotMoleculeById(ids);
    299   }
     198  items = deselected.indexes();
     199  foreach (index, items)
     200    if (index.column() == 0){
     201      int mol_id = model()->data(index, Qt::UserRole).toInt();
     202      if (mol_id < 0)
     203        continue;
     204      //std::cout << "unselect molecule" << std::endl;
     205      MoleCuilder::SelectionNotMoleculeById(mol_id);
     206    }
    300207
    301208  selecting = false;

  • src/UIElements/Views/Qt4/QtMoleculeList.hpp

    r0ac85c3 r7b38d3  
    1414#endif
    1515
     16
    1617#include <QtGui/QTreeWidget>
    17 
    18 #include <map>
    19 #include <string>
    20 
    2118#include "CodePatterns/Observer/Observer.hpp"
    22 
    23 #include "types.hpp"
    2419
    2520class molecule;
    … …  
    3631protected:
    3732  virtual void update(Observable *publisher);
    38   virtual void recieveNotification(Observable *publisher, Notification_ptr notification);
    3933  virtual void subjectKilled(Observable *publisher);
    4034  virtual void paintEvent(QPaintEvent * event);
    … …  
    4236
    4337  static const int COLUMNCOUNT;
    44   enum {NAME,VISIBILITY,ATOMCOUNT,FORMULA,OCCURRENCE,COLUMNTYPES_MAX} COLUMNTYPES;
     38  enum {NAME,ATOMCOUNT,FORMULA,OCCURRENCE,COLUMNTYPES_MAX} COLUMNTYPES;
    4539  static const char *COLUMNNAMES[];
    4640
    4741private slots:
    4842  void moleculeChanged();
    49   void visibilityChanged(QTreeWidgetItem*, int);
    5043
    5144  void rowsSelected(const QItemSelection & selected, const QItemSelection & deselected);
    … …  
    5447  void moleculeSelected(molecule*);
    5548  void moleculeUnSelected(molecule*);
    56   void moleculesVisibilityChanged(const moleculeId_t, bool);
    5749
    5850private:
    … …  
    6052  bool clearing;
    6153  bool selecting;
    62   bool ChangingChildrensVisibility;
    63 
    64   typedef std::map<std::string, unsigned int> FormulaVisibilityCountMap_t;
    65   FormulaVisibilityCountMap_t FormulaVisibilityCountMap;
    66 
    67   typedef std::map<std::string, QTreeWidgetItem*> FormulaTreeItemMap_t;
    68   //!> map of (unique) formulas in the world
    69   FormulaTreeItemMap_t formula;
    7054};
    7155

  • src/UIElements/Views/Qt4/QtToolBar.cpp

    r0ac85c3 r7b38d3  
    2828 */
    2929
     30
     31
     32
    3033// include config.h
    3134#ifdef HAVE_CONFIG_H
    … …  
    3336#endif
    3437
     38
    3539#include "QtToolBar.hpp"
    3640
    3741#include "CodePatterns/MemDebug.hpp"
    3842
    39 #include "CodePatterns/Observer/Notification.hpp"
    40 
    41 #include "Actions/ActionQueue.hpp"
    42 
    4343QtToolBar::QtToolBar(QWidget * _parent) :
    44   QToolBar(_parent),
    45   Observer("QToolBar"),
    46   ActionQueue_observing(false),
    47   undoaction(addActionItem("undo", "undo the last Action", "edit-undo")),
    48   redoaction(addActionItem("redo", "redo the last Action", "edit-redo"))
     44  QToolBar(_parent)
    4945{
    50   // gray out undo/redo buttons initially
    51   undoaction->setEnabled(false);
    52   redoaction->setEnabled(false);
    53 
    54   // sign in
    55   MoleCuilder::ActionQueue::getInstance().signOn(this, MoleCuilder::ActionQueue::ActionQueued);
    56   ActionQueue_observing = true;
     46  addActionItem("undo", "undo the last Action", "edit-undo");
     47  addActionItem("redo", "redo the last Action", "edit-redo");
    5748}
    5849
    … …  
    6051QtToolBar::~QtToolBar()
    6152{
    62   // sign off
    63   if (ActionQueue_observing)
    64     MoleCuilder::ActionQueue::getInstance().signOff(this, MoleCuilder::ActionQueue::ActionQueued);
    6553}
    6654
    6755
    68 QAction * QtToolBar::addActionItem(
    69     const std::string &token,
    70     const std::string &description,
    71     const std::string &icon_name)
     56void QtToolBar::addActionItem(const std::string &token, const std::string &description, const std::string &icon_name)
    7257{
    7358  QAction *action = addAction(QString(description.c_str()));
    … …  
    7863  plumbing.push_back(pipe);
    7964  present_actions.insert( token );
    80   return action;
    8165}
    8266
    … …  
    8872}
    8973
    90 void QtToolBar::update(Observable *publisher)
    91 {
    92   ASSERT(0, "QtToolBar::update() - this should never be called, we are only subscribed to channels.");
    93 }
    94 
    95 void QtToolBar::subjectKilled(Observable *publisher)
    96 {
    97   ActionQueue_observing = false;
    98 }
    99 
    100 void QtToolBar::recieveNotification(Observable *publisher, Notification_ptr notification)
    101 {
    102   if (dynamic_cast<MoleCuilder::ActionQueue *>(publisher) != NULL) {
    103     switch(notification->getChannelNo()) {
    104       case MoleCuilder::ActionQueue::ActionQueued:
    105         undoaction->setEnabled(MoleCuilder::ActionQueue::getInstance().canUndo());
    106         redoaction->setEnabled(MoleCuilder::ActionQueue::getInstance().canRedo());
    107         break;
    108       default:
    109         ASSERT(0, "QtToolBar::recieveNotification() - cannot get here, not subscribed to channel "
    110             +toString(notification->getChannelNo()));
    111         break;
    112     }
    113   } else {
    114     ASSERT(0, "QtToolBar::recieveNotification() - cannot get here, we are only subscribed to ActionQueue.");
    115   }
    116 }

  • src/UIElements/Views/Qt4/QtToolBar.hpp

    r0ac85c3 r7b38d3  
    2727
    2828
    29 class QtToolBar : public QToolBar, public Observer
     29class QtToolBar : public QToolBar
    3030{
    3131  Q_OBJECT
    … …  
    3939   * @param description description to appear as tooltip
    4040   * @param icon_name name of icon
    41    * @return ref to newly created action
    4241   */
    43   QAction * addActionItem(
    44       const std::string &token,
    45       const std::string &description,
    46       const std::string &icon_name);
     42  void addActionItem(const std::string &token, const std::string &description, const std::string &icon_name);
    4743
    4844  /** Function to add a set of favorite actions.
    … …  
    6157  const present_actions_t & getPresentActions() const
    6258  { return present_actions; }
    63 
    64   void update(Observable *publisher);
    65   void subjectKilled(Observable *publisher);
    66   void recieveNotification(Observable *publisher, Notification_ptr notification);
    6759
    6860private:
    … …  
    113105  //!> set of already present action icons
    114106  present_actions_t present_actions;
    115 
    116   //!> sign in to ActionQueue?
    117   bool ActionQueue_observing;
    118   //!> ref to undoaction to gray out
    119   QAction *undoaction;
    120   //!> ref to redoaction to gray out
    121   QAction *redoaction;
    122107};
    123108

  • src/UIElements/Views/Qt4/QtToolBar_QtFavoriteActions.cpp

    r0ac85c3 r7b38d3  
    4646#include "CodePatterns/Assert.hpp"
    4747#include "CodePatterns/Log.hpp"
     48#include "CodePatterns/Observer/Observer.hpp"
    4849
    4950#include "Actions/Action.hpp"

  • src/World.cpp

    r0ac85c3 r7b38d3  
    245245    WorldTime::getInstance().setTime(_step);
    246246
     247    // TODO: removed when BondGraph creates the adjacency
     248    // 3. remove all of World's molecules
     249    for (MoleculeIterator iter = getMoleculeIter();
     250        getMoleculeIter() != moleculeEnd();
     251        iter = getMoleculeIter()) {
     252      getMolecules()->erase(*iter);
     253      destroyMolecule(*iter);
     254    }
     255
    247256    // 4. scan for connected subgraphs => molecules
    248257    DepthFirstSearchAnalysis DFS;
    … …  
    295304
    296305void World::destroyMolecule(molecule* mol){
     306  OBSERVE;
    297307  ASSERT(mol,"Molecule that was meant to be destroyed did not exist");
    298308  destroyMolecule(mol->getId());
    … …  
    309319  }
    310320  mol->signOff(this);
    311   // TODO: removed when depcreated MoleculeListClass is gone
    312   molecules_deprecated->erase(mol);
    313321  DeleteMolecule(mol);
    314322  if (isMoleculeSelected(id))
    … …  
    357365    NOTIFY(AtomRemoved);
    358366  }
    359   // check if it's the last atom
    360   molecule *_mol = atom->getMolecule();
    361   if ((_mol == NULL) || (_mol->getAtomCount() > 1))
    362     _mol = NULL;
    363367  DeleteAtom(atom);
    364368  if (isAtomSelected(id))
    … …  
    366370  atoms.erase(id);
    367371  atomIdPool.releaseId(id);
    368   // remove molecule if empty
    369   if (_mol != NULL)
    370     destroyMolecule(_mol);
    371372}
    372373
    … …  
    554555  std::for_each(invertedSelection.begin(),invertedSelection.end(),
    555556      std::bind1st(std::mem_fun(selector),this)); // func is select... see above
    556 }
    557 
    558 void World::popAtomSelection(){
    559   OBSERVE;
    560   NOTIFY(SelectionChanged);
    561   selectedAtoms = selectedAtoms_Stack.top();
    562   selectedAtoms_Stack.pop();
    563 }
    564 
    565 void World::pushAtomSelection(){
    566   OBSERVE;
    567   NOTIFY(SelectionChanged);
    568   selectedAtoms_Stack.push( selectedAtoms );
    569   selectedAtoms.clear();
    570557}
    571558
    … …  
    698685  std::for_each(invertedSelection.begin(),invertedSelection.end(),
    699686      std::bind1st(std::mem_fun(selector),this)); // func is select... see above
    700 }
    701 
    702 void World::popMoleculeSelection(){
    703   OBSERVE;
    704   NOTIFY(SelectionChanged);
    705   selectedMolecules = selectedMolecules_Stack.top();
    706   selectedMolecules_Stack.pop();
    707 }
    708 
    709 void World::pushMoleculeSelection(){
    710   OBSERVE;
    711   NOTIFY(SelectionChanged);
    712   selectedMolecules_Stack.push( selectedMolecules );
    713   selectedMolecules.clear();
    714687}
    715688

  • src/World.hpp

    r0ac85c3 r7b38d3  
    2020#include <vector>
    2121#include <set>
    22 #include <stack>
    2322#include <boost/thread.hpp>
    2423#include <boost/shared_ptr.hpp>
    … …  
    374373  void clearAtomSelection();
    375374  void invertAtomSelection();
    376   void popAtomSelection();
    377   void pushAtomSelection();
    378375  void selectAtom(const atom*);
    379376  void selectAtom(const atomId_t);
    … …  
    393390  void clearMoleculeSelection();
    394391  void invertMoleculeSelection();
    395   void popMoleculeSelection();
    396   void pushMoleculeSelection();
    397392  void selectMolecule(const molecule*);
    398393  void selectMolecule(const moleculeId_t);
    … …  
    491486  AtomSet atoms;
    492487  AtomSet selectedAtoms;
    493   std::stack<AtomSet> selectedAtoms_Stack;
    494488  /**
    495489   * stores the pool for all available AtomIds below currAtomId
    … …  
    501495  MoleculeSet molecules;
    502496  MoleculeSet selectedMolecules;
    503   std::stack<MoleculeSet> selectedMolecules_Stack;
    504497  /**
    505498   * stores the pool for all available AtomIds below currAtomId

  • src/molecule.cpp

    r0ac85c3 r7b38d3  
    4949#include "CodePatterns/enumeration.hpp"
    5050#include "CodePatterns/Log.hpp"
    51 #include "CodePatterns/Observer/Notification.hpp"
    5251#include "config.hpp"
    5352#include "Descriptors/AtomIdDescriptor.hpp"
    … …  
    147146  OBSERVE;
    148147  if(atomIdPool.reserveId(newNr)){
    149     _lastchangedatom = target;
    150148    NOTIFY(AtomNrChanged);
    151149    if (oldNr != -1)  // -1 is reserved and indicates no number
    … …  
    209207{
    210208  OBSERVE;
     209  NOTIFY(AtomRemoved);
    211210  const_iterator iter = loc;
    212211  ++iter;
    213212  atom * const _atom = const_cast<atom *>(*loc);
    214   {
    215     _lastchangedatom = _atom;
    216     NOTIFY(AtomRemoved);
    217   }
    218213  atomIds.erase( _atom->getId() );
    219214  {
    … …  
    231226{
    232227  OBSERVE;
    233   {
    234     _lastchangedatom = key;
    235     NOTIFY(AtomRemoved);
    236   }
     228  NOTIFY(AtomRemoved);
    237229  const_iterator iter = find(key);
    238230  if (iter != end()){
    … …  
    255247  OBSERVE;
    256248  NOTIFY(AtomInserted);
    257   _lastchangedatom = key;
    258249  std::pair<iterator,bool> res = atomIds.insert(key->getId());
    259250  if (res.second) { // push atom if went well
    … …  
    646637/** Destroys all atoms inside this molecule.
    647638 */
    648 void removeAtomsinMolecule(molecule *&_mol)
     639void molecule::removeAtomsinMolecule()
    649640{
    650641  // remove each atom from world
    651   for(molecule::iterator AtomRunner = _mol->begin(); !_mol->empty(); AtomRunner = _mol->begin())
     642  for(iterator AtomRunner = begin(); !empty(); AtomRunner = begin())
    652643    World::getInstance().destroyAtom(*AtomRunner);
    653   // make sure that pointer os not usable
    654   _mol = NULL;
    655644};
    656645
    … …  
    985974    for(const_iterator iter = begin(); iter != end(); ++iter)
    986975      center += (*iter)->getPosition();
    987     if (begin() != end())
    988       center *= 1./(double)size();
     976    center *= 1./(double)size();
    989977    for(const_iterator iter = begin(); iter != end(); ++iter) {
    990978      const Vector &position = (*iter)->getPosition();
    … …  
    1007995}
    1008996
    1009 void molecule::update(Observable *publisher)
    1010 {
    1011   ASSERT(0, "molecule::update() - did not sign on for any general updates.");
    1012 }
    1013 
    1014 void molecule::recieveNotification(Observable *publisher, Notification_ptr notification)
    1015 {
    1016   const atom * const _atom = dynamic_cast<atom *>(publisher);
    1017   if ((_atom != NULL) && containsAtom(_atom)) {
    1018 #ifdef LOG_OBSERVER
    1019     observerLog().addMessage() << "++ Update of Observer "<< observerLog().getName(static_cast<Observer *>(this))
    1020           << " received notification from atom " << _atom->getId() << " for channel "
    1021           << notification->getChannelNo() << ".";
    1022 #endif
    1023     switch (notification->getChannelNo()) {
    1024       case AtomObservable::PositionChanged:
    1025       {
    1026         // emit others about one of our atoms moved
    1027         _lastchangedatom = const_cast<atom *>(_atom);
    1028         OBSERVE;
    1029         NOTIFY(AtomMoved);
    1030         break;
    1031       }
    1032       default:
    1033         ASSERT( 0, "molecule::recieveNotification() - we did not sign up for channel "
    1034             +toString(notification->getChannelNo()));
    1035         break;
    1036     }
    1037   }
    1038 }
    1039 
    1040 void molecule::subjectKilled(Observable *publisher)
    1041 {
    1042   // do nothing, atom does it all
    1043 }
    1044 
    1045 
    1046997// construct idpool
    1047998CONSTRUCT_IDPOOL(atomId_t, continuousId)

  • src/molecule.hpp

    r0ac85c3 r7b38d3  
    5757/************************************* Class definitions ****************************************/
    5858
    59 /** External function to remove all atoms since this will also delete the molecule
    60  *
    61  * \param _mol ref pointer to molecule to destroy
    62  */
    63 void removeAtomsinMolecule(molecule *&_mol);
    64 
    6559/** The complete molecule.
    6660 * Class incorporates number of types
    … …  
    111105    AtomRemoved,
    112106    AtomNrChanged,
    113     AtomMoved,
    114107    MoleculeNameChanged,
    115108    NotificationType_MAX
    116109  };
    117 
    118   //>! access to last changed element (atom)
    119   const atom* lastChanged() const
    120   { return _lastchangedatom; }
    121110
    122111public:
    … …  
    268257  bool UnlinkAtom(atom *pointer);
    269258  bool CleanupMolecule();
     259  void removeAtomsinMolecule();
    270260
    271261  /// Add/remove atoms to/from molecule.
    … …  
    328318  void flipActiveFlag();
    329319
    330   virtual void update(Observable *publisher);
    331   virtual void recieveNotification(Observable *publisher, Notification_ptr notification);
    332   virtual void subjectKilled(Observable *publisher);
    333 
    334320private:
    335   friend const atom *detail::lastChanged<atom>();
    336   atom *_lastchangedatom;
    337 
    338321  int last_atom; //!< number given to last atom
    339322};

  • tests/regression/Atoms/Translation/testsuite-atoms-translation.at

    r0ac85c3 r7b38d3  
    2424AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/Translation/pre/test.xyz $file], 0)
    2525AT_CHECK([chmod u+w $file], 0)
    26 AT_CHECK([../../molecuilder -i $file --select-all-atoms --translate-atoms --position "1,0,0"], 0, [stdout], [stderr])
     26AT_CHECK([../../molecuilder -i $file --select-all-atoms -t "1,0,0"], 0, [stdout], [stderr])
    2727AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Translation/post/test-shifted.xyz], 0, [ignore], [ignore])
    2828
    … …  
    3636AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/Translation/pre/test.xyz $file], 0)
    3737AT_CHECK([chmod u+w $file], 0)
    38 AT_CHECK([../../molecuilder -i $file --select-all-atoms --translate-atoms --position "1,0,0" --undo], 0, [stdout], [stderr])
     38AT_CHECK([../../molecuilder -i $file --select-all-atoms -t "1,0,0" --undo], 0, [stdout], [stderr])
    3939AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Translation/pre/test.xyz], 0, [ignore], [ignore])
    4040
    … …  
    4848AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/Translation/pre/test.xyz $file], 0)
    4949AT_CHECK([chmod u+w $file], 0)
    50 AT_CHECK([../../molecuilder -i $file --select-all-atoms --translate-atoms --position "1,0,0" --undo --redo], 0, [stdout], [stderr])
     50AT_CHECK([../../molecuilder -i $file --select-all-atoms -t "1,0,0" --undo --redo], 0, [stdout], [stderr])
    5151AT_CHECK([diff -I '.*Created by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Translation/post/test-shifted.xyz], 0, [ignore], [ignore])
    5252

  • tests/regression/Filling/SuspendInWater/pre/test.conf

    r0ac85c3 r7b38d3  
    2828OutSrcStep      5       # Output "restart" data every ..th step
    2929TargetTemp      0.000950045     # Target temperature
    30 MaxPsiStep      3       # number of Minimisation steps per state (0 - default)
     30MaxPsiStep      0       # number of Minimisation steps per state (0 - default)
    3131EpsWannier      1e-07   # tolerance value for spread minimisation of orbitals
    3232
    … …  
    3535RelEpsTotalE    1e-07   # relative change in total energy
    3636RelEpsKineticE  1e-05   # relative change in kinetic energy
    37 MaxMinStopStep  12      # check every ..th steps
    38 MaxMinGapStopStep       1       # check every ..th steps
     37MaxMinStopStep  0       # check every ..th steps
     38MaxMinGapStopStep       0       # check every ..th steps
    3939
    4040# Values specifying when to stop for INIT, otherwise same as above
    … …  
    4242InitRelEpsTotalE        1e-05   # relative change in total energy
    4343InitRelEpsKineticE      0.0001  # relative change in kinetic energy
    44 InitMaxMinStopStep      12      # check every ..th steps
    45 InitMaxMinGapStopStep   1       # check every ..th steps
     44InitMaxMinStopStep      0       # check every ..th steps
     45InitMaxMinGapStopStep   0       # check every ..th steps
    4646
    4747BoxLength                       # (Length of a unit cell)
    … …  
    5555RiemannTensor   0       # (Use metric)
    5656PsiType         0       # 0 - doubly occupied, 1 - SpinUp,SpinDown
    57 MaxPsiDouble    12      # here: specifying both maximum number of SpinUp- and -Down-states
    58 PsiMaxNoUp      12      # here: specifying maximum number of SpinUp-states
    59 PsiMaxNoDown    12      # here: specifying maximum number of SpinDown-states
     57MaxPsiDouble    0       # here: specifying both maximum number of SpinUp- and -Down-states
     58PsiMaxNoUp      0       # here: specifying maximum number of SpinUp-states
     59PsiMaxNoDown    0       # here: specifying maximum number of SpinDown-states
    6060AddPsis         0       # Additional unoccupied Psis for bandgap determination
    6161
    … …  
    6464IsAngstroem     1       # 0 - Bohr, 1 - Angstroem
    6565RelativeCoord   0       # whether ion coordinates are relative (1) or absolute (0)
    66 MaxTypes        3       # maximum number of different ion types
     66MaxTypes        2       # maximum number of different ion types
    6767
    6868# Ion type data (PP = PseudoPotential, Z = atomic number)
    6969#Ion_TypeNr.    Amount  Z       RGauss  L_Max(PP)L_Loc(PP)IonMass       # chemical name, symbol
    70 Ion_Type1       10      1       1.0     3       3       1.00800000000   Hydrogen        H
     70Ion_Type1       8       1       1.0     3       3       1.00800000000   Hydrogen        H
    7171Ion_Type2       3       6       1.0     3       3       12.01100000000  Carbon  C
    72 Ion_Type3       1       8       1.0     3       3       15.99900000000  Oxygen  O
    7372#Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)
    74 Ion_Type1_1     9.782085945     2.645886050     2.645886050     0 # molecule nr 0
    75 Ion_Type1_2     9.782085945     2.645886050     4.425886024     0 # molecule nr 1
    76 Ion_Type1_3     10.672039608    3.904536878     3.535886037     0 # molecule nr 2
    77 Ion_Type1_4     8.532785963     4.787886018     2.645886050     0 # molecule nr 3
    78 Ion_Type1_5     8.532785963     4.787886018     4.425886024     0 # molecule nr 4
    79 Ion_Type1_6     6.393632318     3.904536877     3.535886037     0 # molecule nr 5
    80 Ion_Type1_7     7.283585982     2.645886050     2.645886050     0 # molecule nr 6
    81 Ion_Type1_8     7.283585982     2.645886050     4.425886024     0 # molecule nr 7
    82 Ion_Type2_1     9.782085945     3.275186040     3.535886037     0 # molecule nr 8
    83 Ion_Type2_2     8.532785963     4.158586027     3.535886037     0 # molecule nr 9
    84 Ion_Type2_3     7.283585982     3.275186040     3.535886037     0 # molecule nr 10
    85 Ion_Type3_1     2.000000000     2.000000000     2.000000000     0 # molecule nr 11
    86 Ion_Type1_9     2.758602000     2.000000000     2.504284000     0 # molecule nr 12
    87 Ion_Type1_10    2.758602000     2.000000000     1.495716000     0 # molecule nr 13
     73Ion_Type2_1     9.782085945     3.275186040     3.535886037     0 # molecule nr 0
     74Ion_Type2_2     8.532785963     4.158586027     3.535886037     0 # molecule nr 1
     75Ion_Type2_3     7.283585982     3.275186040     3.535886037     0 # molecule nr 2
     76Ion_Type1_1     9.782085945     2.645886050     2.645886050     0 # molecule nr 3
     77Ion_Type1_2     9.782085945     2.645886050     4.425886024     0 # molecule nr 4
     78Ion_Type1_3     10.672039608    3.904536878     3.535886037     0 # molecule nr 5
     79Ion_Type1_4     8.532785963     4.787886018     2.645886050     0 # molecule nr 6
     80Ion_Type1_5     8.532785963     4.787886018     4.425886024     0 # molecule nr 7
     81Ion_Type1_6     6.393632318     3.904536877     3.535886037     0 # molecule nr 8
     82Ion_Type1_7     7.283585982     2.645886050     2.645886050     0 # molecule nr 9
     83Ion_Type1_8     7.283585982     2.645886050     4.425886024     0 # molecule nr 10

  • tests/regression/Filling/SuspendInWater/testsuite-suspend-in-water.at

    r0ac85c3 r7b38d3  
    1818### suspend in water with certain density
    1919
    20 AT_SETUP([Filling - suspend in water fails with rho=1])
     20AT_SETUP([Filling - suspend in water])
     21AT_XFAIL_IF([/bin/true])
    2122AT_KEYWORDS([filling suspend-in-water])
    2223
    … …  
    2425AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/pre/test.conf $file], 0)
    2526AT_CHECK([chmod u+w $file], 0)
    26 AT_CHECK([../../molecuilder -i $file -I -v 3 --select-molecule-by-id 0 -u --density 1.], 5, [stdout], [stderr])
     27AT_CHECK([../../molecuilder -i $file  -v 3 --select-molecule-by-id 0 -u 1.3], 0, [stdout], [stderr])
     28AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/post/test.conf], 0, [ignore], [ignore])
    2729
    2830AT_CLEANUP
    2931
    30 AT_SETUP([Filling - suspend in water fails with just one molecule])
    31 AT_KEYWORDS([filling suspend-in-water])
    32 
    33 file=single_molecule.conf
    34 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/pre/$file $file], 0)
    35 AT_CHECK([chmod u+w $file], 0)
    36 AT_CHECK([../../molecuilder -i $file -I -v 3 --select-molecule-by-id 0 -u --density 1.], 5, [stdout], [stderr])
    37 AT_CHECK([grep "at least two molecules" stdout], 0, [ignore], [ignore])
    38 
    39 AT_CLEANUP
    40 
    41 # rho must be on same side of 1 as the present density
    42 AT_SETUP([Filling - suspend in water fails with wrong rho])
    43 AT_KEYWORDS([filling suspend-in-water])
    44 
    45 file=test.conf
    46 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/pre/$file $file], 0)
    47 AT_CHECK([chmod u+w $file], 0)
    48 AT_CHECK([../../molecuilder -i $file -I -v 3 --select-molecule-by-id 0 -u --density .5], 5, [stdout], [stderr])
    49 AT_CHECK([grep "Desired and present molecular densities must both be either" stdout], 0, [ignore], [ignore])
    50 
    51 AT_CLEANUP
    52 
    53 AT_SETUP([Filling - suspend in water])
    54 AT_XFAIL_IF([/bin/true])
    55 AT_KEYWORDS([filling suspend-in-water])
    56 
    57 file=test.conf
    58 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/pre/$file $file], 0)
    59 AT_CHECK([chmod u+w $file], 0)
    60 AT_CHECK([../../molecuilder -i $file -I -v 3 --select-molecule-by-id 0 -u --density 2.], 5, [stdout], [stderr])
    61 AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/post/test.conf], 0, [ignore], [ignore])
    62 
    63 AT_CLEANUP
    6432
    6533AT_SETUP([Filling - suspend in water with Undo])
    … …  
    7038AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/pre/test.conf $file], 0)
    7139AT_CHECK([chmod u+w $file], 0)
    72 AT_CHECK([../../molecuilder -i $file -I -v 3 --select-molecule-by-id 0 -u --density 2. --undo], 0, [stdout], [stderr])
     40AT_CHECK([../../molecuilder -i $file  -v 3 --select-molecule-by-id 0 -u 1.3 --undo], 0, [stdout], [stderr])
    7341AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/post/test.conf], 0, [ignore], [ignore])
    7442
    … …  
    8351AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/pre/test.conf $file], 0)
    8452AT_CHECK([chmod u+w $file], 0)
    85 AT_CHECK([../../molecuilder -i $file -I -v 3 --select-molecule-by-id 0 -u --density 2. --undo --redo], 0, [stdout], [stderr])
     53AT_CHECK([../../molecuilder -i $file  -v 3 --select-molecule-by-id 0 -u 1.3 --undo --redo], 0, [stdout], [stderr])
    8654AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Filling/SuspendInWater/post/test.conf], 0, [ignore], [ignore])
    8755

  • tests/regression/Makefile.am

    r0ac85c3 r7b38d3  
    9898        $(srcdir)/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at \
    9999        $(srcdir)/Molecules/LinearInterpolationofTrajectories/testsuite-molecules-linear-interpolation-of-trajectories.at \
    100         $(srcdir)/Molecules/Remove/testsuite-molecules-remove.at \
    101100        $(srcdir)/Molecules/RotateAroundOrigin/testsuite-molecules-rotate-around-origin.at \
    102101        $(srcdir)/Molecules/RotateAroundSelf/testsuite-molecules-rotate-around-self.at \
    … …  
    202201        $(srcdir)/Selection/Atoms/ClearAtoms/testsuite-selection-clear-atoms.at \
    203202        $(srcdir)/Selection/Atoms/InvertAtoms/testsuite-selection-invert-atoms.at \
    204         $(srcdir)/Selection/Atoms/PopAtomSelection/testsuite-selection-pop-atom-selection.at \
    205         $(srcdir)/Selection/Atoms/PushAtomSelection/testsuite-selection-push-atom-selection.at \
    206203        $(srcdir)/Selection/Molecules/testsuite-selection-molecules.at \
    207204        $(srcdir)/Selection/Molecules/AllMolecules/testsuite-selection-select-all-molecules.at \
    … …  
    221218        $(srcdir)/Selection/Molecules/MoleculeOfAtom/testsuite-selection-select-atoms-molecules.at \
    222219        $(srcdir)/Selection/Molecules/MoleculeOfAtom/testsuite-selection-unselect-atoms-molecules.at \
    223         $(srcdir)/Selection/Molecules/PopMoleculeSelection/testsuite-selection-pop-molecule-selection.at \
    224         $(srcdir)/Selection/Molecules/PushMoleculeSelection/testsuite-selection-push-molecule-selection.at \
    225220        $(srcdir)/Tesselation/testsuite-tesselation.at \
    226221        $(srcdir)/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at \

  • tests/regression/Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at

    r0ac85c3 r7b38d3  
    11#
    22#    MoleCuilder - creates and alters molecular systems
    3 #    Copyright (C) 2014 Frederik Heber
     3#    Copyright (C) 2008-2012 University of Bonn
    44#
    55#    This program is free software: you can redistribute it and/or modify
    … …  
    1919
    2020AT_SETUP([Molecules - Translation with periodic boundaries])
    21 AT_KEYWORDS([molecules translate-molecules])
     21AT_KEYWORDS([molecules translate-atoms])
    2222
    2323file=test.conf
    2424AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/Translation-Periodic/pre/test.conf $file], 0)
    2525AT_CHECK([chmod u+w $file], 0)
    26 AT_CHECK([../../molecuilder -i $file  --select-molecule-by-id 0 --translate-molecules --position "-8., -8., -8." --periodic 1], 0, [stdout], [stderr])
     26AT_CHECK([../../molecuilder -i $file  --select-molecule-by-id 0 --select-molecules-atoms -t "-8., -8., -8." --periodic 1], 0, [stdout], [stderr])
    2727AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Molecules/Translation-Periodic/post/test.conf], 0, [ignore], [ignore])
    2828
    … …  
    3131
    3232AT_SETUP([Molecules - Translation with periodic boundaries with Undo])
    33 AT_KEYWORDS([molecules translate-molecules undo])
     33AT_KEYWORDS([molecules translate-atoms undo])
    3434
    3535file=test.conf
    3636AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/Translation-Periodic/pre/test.conf $file], 0)
    3737AT_CHECK([chmod u+w $file], 0)
    38 AT_CHECK([../../molecuilder -i $file  --select-molecule-by-id 0 --translate-molecules --position "-8., -8., -8." --periodic 1 --undo], 0, [stdout], [stderr])
     38AT_CHECK([../../molecuilder -i $file  --select-molecule-by-id 0 --select-molecules-atoms -t "-8., -8., -8." --periodic 1 --undo], 0, [stdout], [stderr])
    3939AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Molecules/Translation-Periodic/post/test-undo.conf], 0, [ignore], [ignore])
    4040
    … …  
    4343
    4444AT_SETUP([Molecules - Translation with periodic boundaries with Redo])
    45 AT_KEYWORDS([molecules translate-molecules redo])
     45AT_KEYWORDS([molecules translate-atoms redo])
    4646
    4747file=test.conf
    4848AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/Translation-Periodic/pre/test.conf $file], 0)
    4949AT_CHECK([chmod u+w $file], 0)
    50 AT_CHECK([../../molecuilder -i $file  --select-molecule-by-id 0 --translate-molecules --position "-8., -8., -8." --periodic 1 --undo --redo], 0, [stdout], [stderr])
     50AT_CHECK([../../molecuilder -i $file  --select-molecule-by-id 0 --select-molecules-atoms -t "-8., -8., -8." --periodic 1 --undo --redo], 0, [stdout], [stderr])
    5151AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Molecules/Translation-Periodic/post/test.conf], 0, [ignore], [ignore])
    5252

  • tests/regression/Molecules/Translation/testsuite-molecules-translation.at

    r0ac85c3 r7b38d3  
    11#
    22#    MoleCuilder - creates and alters molecular systems
    3 #    Copyright (C) 2014 Frederik Heber
     3#    Copyright (C) 2008-2012 University of Bonn
    44#
    55#    This program is free software: you can redistribute it and/or modify
    … …  
    1919
    2020AT_SETUP([Molecules - Translation])
    21 AT_KEYWORDS([molecules translate-molecules])
     21AT_KEYWORDS([molecules translate-atoms])
    2222
    2323file=test.conf
    2424AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/Translation/pre/test.conf $file], 0)
    2525AT_CHECK([chmod u+w $file], 0)
    26 AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 --translate-molecules --position "1., 1., 1." --periodic 0], 0, [stdout], [stderr])
     26AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 --select-molecules-atoms -t "1., 1., 1." --periodic 0], 0, [stdout], [stderr])
    2727AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Molecules/Translation/post/test.conf], 0, [ignore], [ignore])
    2828
    … …  
    3030AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/Translation/pre/test2.conf $file], 0)
    3131AT_CHECK([chmod u+w $file], 0)
    32 AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 --translate-molecules --position "-1., -1., -1." --periodic 0], 0, [stdout], [stderr])
     32AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 --select-molecules-atoms -t "-1., -1., -1." --periodic 0], 0, [stdout], [stderr])
    3333AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Molecules/Translation/post/test2.conf], 0, [ignore], [ignore])
    3434
    … …  
    3737
    3838AT_SETUP([Molecules - Translation with Undo])
    39 AT_KEYWORDS([molecules translate-molecules undo])
     39AT_KEYWORDS([molecules translate-atoms undo])
    4040
    4141file=test.conf
    4242AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/Translation/pre/test.conf $file], 0)
    4343AT_CHECK([chmod u+w $file], 0)
    44 AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 --translate-molecules --position "1., 1., 1." --periodic 0 --undo], 0, [stdout], [stderr])
     44AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 --select-molecules-atoms -t "1., 1., 1." --periodic 0 --undo], 0, [stdout], [stderr])
    4545AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Molecules/Translation/post/test-undo.conf], 0, [ignore], [ignore])
    4646
    … …  
    4848AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/Translation/pre/test2.conf $file], 0)
    4949AT_CHECK([chmod u+w $file], 0)
    50 AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 --translate-molecules --position "-1., -1., -1." --periodic 0 --undo], 0, [stdout], [stderr])
     50AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 --select-molecules-atoms -t "-1., -1., -1." --periodic 0 --undo], 0, [stdout], [stderr])
    5151AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Molecules/Translation/post/test2-undo.conf], 0, [ignore], [ignore])
    5252
    … …  
    5555
    5656AT_SETUP([Molecules - Translation with Redo])
    57 AT_KEYWORDS([molecules translate-molecules redo])
     57AT_KEYWORDS([molecules translate-atoms redo])
    5858
    5959file=test.conf
    6060AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/Translation/pre/test.conf $file], 0)
    6161AT_CHECK([chmod u+w $file], 0)
    62 AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 --translate-molecules --position "1., 1., 1." --periodic 0 --undo --redo], 0, [stdout], [stderr])
     62AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 --select-molecules-atoms -t "1., 1., 1." --periodic 0 --undo --redo], 0, [stdout], [stderr])
    6363AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Molecules/Translation/post/test.conf], 0, [ignore], [ignore])
    6464
    … …  
    6666AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Molecules/Translation/pre/test2.conf $file], 0)
    6767AT_CHECK([chmod u+w $file], 0)
    68 AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 --translate-molecules --position "-1., -1., -1." --periodic 0 --undo --redo], 0, [stdout], [stderr])
     68AT_CHECK([../../molecuilder -i $file --select-molecule-by-id 0 --select-molecules-atoms -t "-1., -1., -1." --periodic 0 --undo --redo], 0, [stdout], [stderr])
    6969AT_CHECK([diff $file ${abs_top_srcdir}/tests/regression/Molecules/Translation/post/test2.conf], 0, [ignore], [ignore])
    7070

  • tests/regression/Molecules/testsuite-molecules.at

    r0ac85c3 r7b38d3  
    5454m4_include([Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at])
    5555
    56 # remove whole molecules
    57 m4_include([Molecules/Remove/testsuite-molecules-remove.at])
    58 
    5956# Rotate to Principal Axis System
    6057m4_include([Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at])

  • tests/regression/Options/InvalidCommands/testsuite-options-invalid-commands.at

    r0ac85c3 r7b38d3  
    2424AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Options/InvalidCommands/pre/test.conf $file], 0)
    2525AT_CHECK([chmod u+w $file], 0)
     26AT_CHECK([../../molecuilder -i $file  -t], 134, [ignore], [stderr])
    2627AT_CHECK([../../molecuilder -i $file  -s -b -E -c -b -a], 134, [ignore], [stderr])
    2728AT_CHECK([../../molecuilder -i $file  -b -E -c -b -a], 134, [ignore], [stderr])

  • tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load-multiply.at

    r0ac85c3 r7b38d3  
    2424destfile=doublewater.in
    2525AT_CHECK([../../molecuilder -i $destfile -o mpqc -l ${abs_top_srcdir}/tests/regression/Parser/Mpqc/pre/$srcfile], 0, [ignore], [ignore])
    26 AT_CHECK([../../molecuilder -i $destfile -l ${abs_top_srcdir}/tests/regression/Parser/Mpqc/pre/$srcfile --select-molecule-by-order -1 --select-molecules-atoms --translate-atoms --position "2,0,0"], 0, [ignore], [ignore])
     26AT_CHECK([../../molecuilder -i $destfile -l ${abs_top_srcdir}/tests/regression/Parser/Mpqc/pre/$srcfile --select-molecule-by-order -1 --select-molecules-atoms --translate-atoms "2,0,0"], 0, [ignore], [ignore])
    2727AT_CHECK([diff -I '%.*' $destfile ${abs_top_srcdir}/tests/regression/Parser/Mpqc/post/$destfile], 0, [ignore], [ignore])
    2828

  • tests/regression/Parser/Pcp/testsuite-parser-pcp-load-multiply.at

    r0ac85c3 r7b38d3  
    2424destfile=doublewater.conf
    2525AT_CHECK([../../molecuilder -i $destfile -o pcp -l ${abs_top_srcdir}/tests/regression/Parser/Pcp/pre/$srcfile], 0, [ignore], [ignore])
    26 AT_CHECK([../../molecuilder -i $destfile -l ${abs_top_srcdir}/tests/regression/Parser/Pcp/pre/$srcfile --select-molecule-by-order -1 --select-molecules-atoms --translate-atoms --position "2,0,0"], 0, [ignore], [ignore])
     26AT_CHECK([../../molecuilder -i $destfile -l ${abs_top_srcdir}/tests/regression/Parser/Pcp/pre/$srcfile --select-molecule-by-order -1 --select-molecules-atoms --translate-atoms "2,0,0"], 0, [ignore], [ignore])
    2727AT_CHECK([diff $destfile ${abs_top_srcdir}/tests/regression/Parser/Pcp/post/$destfile], 0, [ignore], [ignore])
    2828

  • tests/regression/Parser/Pdb/testsuite-parser-pdb-load-multiply.at

    r0ac85c3 r7b38d3  
    2424destfile=doublewater.pdb
    2525AT_CHECK([../../molecuilder -i $destfile -o pdb -l ${abs_top_srcdir}/tests/regression/Parser/Pdb/pre/$srcfile], 0, [ignore], [ignore])
    26 AT_CHECK([../../molecuilder -i $destfile -l ${abs_top_srcdir}/tests/regression/Parser/Pdb/pre/$srcfile --select-molecule-by-order -1 --select-molecules-atoms --translate-atoms --position "2,0,0"], 0, [ignore], [ignore])
     26AT_CHECK([../../molecuilder -i $destfile -l ${abs_top_srcdir}/tests/regression/Parser/Pdb/pre/$srcfile --select-molecule-by-order -1 --select-molecules-atoms --translate-atoms "2,0,0"], 0, [ignore], [ignore])
    2727AT_CHECK([diff -I 'REMARK.*' $destfile ${abs_top_srcdir}/tests/regression/Parser/Pdb/post/$destfile], 0, [ignore], [ignore])
    2828

  • tests/regression/Parser/Psi3/testsuite-parser-psi3-load-multiply.at

    r0ac85c3 r7b38d3  
    2424destfile=doublewater.psi
    2525AT_CHECK([../../molecuilder -i $destfile -o psi3 -l ${abs_top_srcdir}/tests/regression/Parser/Psi3/pre/$srcfile], 0, [ignore], [ignore])
    26 AT_CHECK([../../molecuilder -i $destfile -l ${abs_top_srcdir}/tests/regression/Parser/Psi3/pre/$srcfile --select-molecule-by-order -1 --select-molecules-atoms --translate-atoms --position "2,0,0"], 0, [ignore], [ignore])
     26AT_CHECK([../../molecuilder -i $destfile -l ${abs_top_srcdir}/tests/regression/Parser/Psi3/pre/$srcfile --select-molecule-by-order -1 --select-molecules-atoms --translate-atoms "2,0,0"], 0, [ignore], [ignore])
    2727AT_CHECK([diff -w -I '%.*' $destfile ${abs_top_srcdir}/tests/regression/Parser/Psi3/post/$destfile], 0, [ignore], [ignore])
    2828

  • tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load-multiply.at

    r0ac85c3 r7b38d3  
    2525destfile=doublewater.data
    2626AT_CHECK([../../molecuilder -i $destfile -o tremolo -l ${abs_top_srcdir}/tests/regression/Parser/Tremolo/pre/$srcfile], 0, [ignore], [ignore])
    27 AT_CHECK([../../molecuilder -i $destfile -l ${abs_top_srcdir}/tests/regression/Parser/Tremolo/pre/$srcfile --select-molecule-by-order -1 --select-molecules-atoms --translate-atoms --position "2,0,0"], 0, [ignore], [ignore])
     27AT_CHECK([../../molecuilder -i $destfile -l ${abs_top_srcdir}/tests/regression/Parser/Tremolo/pre/$srcfile --select-molecule-by-order -1 --select-molecules-atoms --translate-atoms "2,0,0"], 0, [ignore], [ignore])
    2828AT_CHECK([diff -w -I '#.*' $destfile ${abs_top_srcdir}/tests/regression/Parser/Tremolo/post/$destfile], 0, [ignore], [ignore])
    2929

  • tests/regression/Parser/Xyz/testsuite-parser-xyz-load-multiply.at

    r0ac85c3 r7b38d3  
    2424destfile=doublewater.xyz
    2525AT_CHECK([../../molecuilder -i $destfile -o xyz -l ${abs_top_srcdir}/tests/regression/Parser/Xyz/pre/$srcfile], 0, [ignore], [ignore])
    26 AT_CHECK([../../molecuilder -i $destfile -l ${abs_top_srcdir}/tests/regression/Parser/Xyz/pre/$srcfile --select-molecule-by-order -1 --select-molecules-atoms --translate-atoms --position "2,0,0"], 0, [ignore], [ignore])
     26AT_CHECK([../../molecuilder -i $destfile -l ${abs_top_srcdir}/tests/regression/Parser/Xyz/pre/$srcfile --select-molecule-by-order -1 --select-molecules-atoms --translate-atoms "2,0,0"], 0, [ignore], [ignore])
    2727AT_CHECK([diff -I '.*Created by molecuilder.*' $destfile ${abs_top_srcdir}/tests/regression/Parser/Xyz/post/$destfile], 0, [ignore], [ignore])
    2828

  • tests/regression/Selection/Atoms/testsuite-selection-atoms.at

    r0ac85c3 r7b38d3  
    5959m4_include(Selection/Atoms/InvertAtoms/testsuite-selection-invert-atoms.at)
    6060
    61 # push atom selection
    62 m4_include(Selection/Atoms/PushAtomSelection/testsuite-selection-push-atom-selection.at)
    63 
    64 # pop atom selection
    65 m4_include(Selection/Atoms/PopAtomSelection/testsuite-selection-pop-atom-selection.at)

  • tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-select-molecule-by-id.at

    r0ac85c3 r7b38d3  
    2525srcfile=box.xyz
    2626testfile=test.xyz
    27 targetfile=water_id2_4.xyz
     27targetfile=water_id4.xyz
    2828AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
    29 AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 2 4 -s $targetfile], 0, [stdout], [stderr])
     29AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 4 -s $targetfile], 0, [stdout], [stderr])
    3030AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
    3131
    … …  
    4141targetfile=empty.xyz
    4242AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
    43 AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 2 4 --undo -s $targetfile], 0, [stdout], [stderr])
     43AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 4 --undo -s $targetfile], 0, [stdout], [stderr])
    4444AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
    4545
    … …  
    5353srcfile=box.xyz
    5454testfile=test.xyz
    55 targetfile=water_id2_4.xyz
     55targetfile=water_id4.xyz
    5656AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
    57 AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 2 4 --undo --redo -s $targetfile], 0, [stdout], [stderr])
     57AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 4 --undo --redo -s $targetfile], 0, [stdout], [stderr])
    5858AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
    5959

  • tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-unselect-molecule-by-id.at

    r0ac85c3 r7b38d3  
    2525srcfile=box.xyz
    2626testfile=test.xyz
    27 targetfile=id2_4_missing.xyz
     27targetfile=id4_missing.xyz
    2828AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
    29 AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 2 4 -s $targetfile], 0, [stdout], [stderr])
     29AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 4 -s $targetfile], 0, [stdout], [stderr])
    3030AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
    3131
    … …  
    4141targetfile=box.xyz
    4242AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
    43 AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 2 4 --undo -s $targetfile], 0, [stdout], [stderr])
     43AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 4 --undo -s $targetfile], 0, [stdout], [stderr])
    4444AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
    4545
    … …  
    5353srcfile=box.xyz
    5454testfile=test.xyz
    55 targetfile=id2_4_missing.xyz
     55targetfile=id4_missing.xyz
    5656AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
    57 AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 2 4 --undo --redo -s $targetfile], 0, [stdout], [stderr])
     57AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 4 --undo --redo -s $targetfile], 0, [stdout], [stderr])
    5858AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
    5959

  • tests/regression/Selection/Molecules/testsuite-selection-molecules.at

    r0ac85c3 r7b38d3  
    5252m4_include(Selection/Molecules/InvertMolecules/testsuite-selection-invert-molecules.at)
    5353
    54 # push molecule selection
    55 m4_include(Selection/Molecules/PushMoleculeSelection/testsuite-selection-push-molecule-selection.at)
    56 
    57 # pop molecule selection
    58 m4_include(Selection/Molecules/PopMoleculeSelection/testsuite-selection-pop-molecule-selection.at)
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