Changeset 2affd1 for src


Ignore:
Timestamp:
Feb 11, 2016, 8:07:11 AM (10 years ago)
Author:
Frederik Heber <heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, Candidate_v1.7.0, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable
Children:
eb6552
Parents:
df5b8c
git-author:
Frederik Heber <heber@…> (12/30/15 10:02:58)
git-committer:
Frederik Heber <heber@…> (02/11/16 08:07:11)
Message:

Removed molecules_deprecated from World and unnecessary includes of MoleculeListClass and all insert/erase.

  • this goes along the lines of removing "remove me when we don't need MoleculeCistClass anymore".
Location:
src
Files:
40 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/FillAction/FillRegularGridAction.cpp

    rdf5b8c r2affd1  
    4646#include "Filling/Preparators/BoxFillerPreparator.hpp"
    4747#include "molecule.hpp"
    48 #include "MoleculeListClass.hpp"
    4948#include "Parser/FormatParserInterface.hpp"
    5049#include "Parser/FormatParserStorage.hpp"

  • src/Actions/FillAction/FillVolumeAction.cpp

    rdf5b8c r2affd1  
    4646#include "Filling/Preparators/ShapeVolumeFillerPreparator.hpp"
    4747#include "molecule.hpp"
    48 #include "MoleculeListClass.hpp"
    4948#include "Parser/FormatParserInterface.hpp"
    5049#include "Parser/FormatParserStorage.hpp"

  • src/Actions/FillAction/SuspendInMoleculeAction.cpp

    rdf5b8c r2affd1  
    4949#include "LinkedCell/PointCloudAdaptor.hpp"
    5050#include "molecule.hpp"
    51 #include "MoleculeListClass.hpp"
    5251#include "Parser/FormatParserInterface.hpp"
    5352#include "Parser/FormatParserStorage.hpp"

  • src/Actions/GraphAction/UpdateMoleculesAction.cpp

    rdf5b8c r2affd1  
    4646#include "Graph/DepthFirstSearchAnalysis.hpp"
    4747#include "molecule.hpp"
    48 #include "MoleculeListClass.hpp"
    4948#include "World.hpp"
    5049
    … …  
    8382  // 0a. remove all present molecules
    8483  LOG(0, "STATUS: Removing all present molecules.");
    85   MoleculeListClass *molecules = World::getInstance().getMolecules();
    8684  vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
    87   for (vector<molecule *>::iterator MolRunner = allmolecules.begin(); MolRunner != allmolecules.end(); ++MolRunner) {
    88     molecules->erase(*MolRunner);
     85  for (vector<molecule *>::iterator MolRunner = allmolecules.begin();
     86      MolRunner != allmolecules.end();
     87      ++MolRunner)
    8988    World::getInstance().destroyMolecule(*MolRunner);
    90   }
    9189
    9290  // 2. scan for connected subgraphs
    … …  
    112110  {
    113111    // remove all present molecules
    114     MoleculeListClass *molecules = World::getInstance().getMolecules();
    115112    vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
    116     for (vector<molecule *>::iterator MolRunner = allmolecules.begin(); MolRunner != allmolecules.end(); ++MolRunner) {
    117       molecules->erase(*MolRunner);
     113    for (vector<molecule *>::iterator MolRunner = allmolecules.begin();
     114        MolRunner != allmolecules.end();
     115        ++MolRunner)
    118116      World::getInstance().destroyMolecule(*MolRunner);
    119     }
    120117  }
    121118
    122119  {
    123120    // construct the old state
    124     MoleculeListClass *molecules = World::getInstance().getMolecules();
    125121    molecule *mol = NULL;
    126122    for (MolAtomList::const_iterator iter = state->moleculelist.begin(); iter != state->moleculelist.end(); ++iter) {
    … …  
    132128        mol->AddAtom(Walker);
    133129      }
    134       molecules->insert(mol);
    135130    }
    136131  }

  • src/Actions/MoleculeAction/BondFileAction.def

    rdf5b8c r2affd1  
    77
    88// all includes and forward declarations necessary for non-integral types below
    9 class MoleculeListClass;
    10 
    119#include "Parameters/Validators/DummyValidator.hpp"
    1210#include "Parameters/Validators/Specific/FilePresentValidator.hpp"

  • src/Actions/MoleculeAction/ChangeNameAction.def

    rdf5b8c r2affd1  
    77
    88// all includes and forward declarations necessary for non-integral types below
    9 class MoleculeListClass;
    10 
    119#include "Parameters/Validators/DummyValidator.hpp"
    1210

  • src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def

    rdf5b8c r2affd1  
    77
    88// all includes and forward declarations necessary for non-integral types below
    9 class MoleculeListClass;
    10 
    119#include "Parameters/Validators/DummyValidator.hpp"
    1210#include "Parameters/Validators/GenericValidators.hpp"

  • src/Actions/MoleculeAction/LoadAction.cpp

    rdf5b8c r2affd1  
    3838#include "CodePatterns/Verbose.hpp"
    3939#include "Descriptors/MoleculeIdDescriptor.hpp"
     40#include "Descriptors/MoleculeOrderDescriptor.hpp"
    4041#include "Parser/Exceptions.hpp"
    4142#include "Parser/FormatParserInterface.hpp"
    … …  
    4344#include "Parser/FormatParser_Parameters.hpp"
    4445#include "molecule.hpp"
    45 #include "MoleculeListClass.hpp"
    4646#include "World.hpp"
    4747
    … …  
    102102
    103103    // set file name of last molecule
    104     MoleculeList::const_reverse_iterator iter = World::getInstance().getMolecules()->ListOfMolecules.rbegin();
    105     (*iter)->SetNameFromFilename(FilenamePrefix.c_str());
    106     LOG(0, "Chemical formula is " << (*iter)->getFormula());
     104    molecule * const mol = World::getInstance().getMolecule(MoleculeByOrder(-1));
     105    mol->SetNameFromFilename(FilenamePrefix.c_str());
     106    LOG(0, "Chemical formula is " << mol->getFormula());
    107107
    108108    return ActionState::ptr(
    109         new MoleculeLoadState((*iter)->getId(),FilenamePrefix,FilenameSuffix,boost::shared_ptr<FormatParser_Parameters>(ParserParams),params)
     109        new MoleculeLoadState(mol->getId(),FilenamePrefix,FilenameSuffix,boost::shared_ptr<FormatParser_Parameters>(ParserParams),params)
    110110    );
    111111  }
    … …  
    151151
    152152  // set file name of last molecule
    153   MoleculeList::const_reverse_iterator iter = World::getInstance().getMolecules()->ListOfMolecules.rbegin();
    154   (*iter)->SetNameFromFilename(state->FilenamePrefix.c_str());
    155   (*iter)->setId(state->molId);
    156   LOG(0, "Chemical formula is " << (*iter)->getFormula());
     153  molecule * const mol = World::getInstance().getMolecule(MoleculeByOrder(-1));
     154  mol->SetNameFromFilename(state->FilenamePrefix.c_str());
     155  mol->setId(state->molId);
     156  LOG(0, "Chemical formula is " << mol->getFormula());
    157157
    158158  return ActionState::ptr(
    159       new MoleculeLoadState((*iter)->getId(),state->FilenamePrefix,state->FilenameSuffix,boost::shared_ptr<FormatParser_Parameters>(ParserParams),params)
     159      new MoleculeLoadState(mol->getId(),state->FilenamePrefix,state->FilenameSuffix,boost::shared_ptr<FormatParser_Parameters>(ParserParams),params)
    160160  );
    161161}

  • src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def

    rdf5b8c r2affd1  
    77
    88// all includes and forward declarations necessary for non-integral types below
    9 class MoleculeListClass;
    109class Vector;
    1110

  • src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def

    rdf5b8c r2affd1  
    99#include "Actions/Values.hpp"
    1010#include "LinearAlgebra/Vector.hpp"
    11 
    12 class MoleculeListClass;
    1311
    1412#include "Parameters/Validators/Specific/VectorNotZeroValidator.hpp"

  • src/Actions/MoleculeAction/SaveAdjacencyAction.def

    rdf5b8c r2affd1  
    77
    88// all includes and forward declarations necessary for non-integral types below
    9 class MoleculeListClass;
    10 
    119#include "Parameters/Validators/Ops_Validator.hpp"
    1210#include "Parameters/Validators/Specific/FilePresentValidator.hpp"

  • src/Actions/MoleculeAction/SaveBondsAction.def

    rdf5b8c r2affd1  
    77
    88// all includes and forward declarations necessary for non-integral types below
    9 class MoleculeListClass;
    10 
    119#include "Parameters/Validators/Ops_Validator.hpp"
    1210#include "Parameters/Validators/Specific/FilePresentValidator.hpp"

  • src/Actions/MoleculeAction/SaveTemperatureAction.def

    rdf5b8c r2affd1  
    77
    88// all includes and forward declarations necessary for non-integral types below
    9 class MoleculeListClass;
    10 
    119#include "Parameters/Validators/Ops_Validator.hpp"
    1210#include "Parameters/Validators/Specific/FilePresentValidator.hpp"

  • src/Actions/WorldAction/InputAction.cpp

    rdf5b8c r2affd1  
    3636
    3737#include "CodePatterns/Log.hpp"
     38
     39#include "Descriptors/MoleculeOrderDescriptor.hpp"
    3840#include "molecule.hpp"
    39 #include "MoleculeListClass.hpp"
    4041#include "Parser/Exceptions.hpp"
    4142#include "Parser/FormatParserStorage.hpp"
    … …  
    5758/** =========== define the function ====================== */
    5859ActionState::ptr WorldInputAction::performCall() {
    59 //  MoleculeListClass *molecules = World::getInstance().getMolecules();
    60 //  molecule *mol = NULL;
    6160  boost::filesystem::ifstream test;
    6261  FormatParserStorage &parsers = FormatParserStorage::getInstance();
    … …  
    9998
    10099    // set file name of last molecule
    101     MoleculeList::const_iterator iter = World::getInstance().getMolecules()->ListOfMolecules.end();
    102     iter--;
    103     (*iter)->SetNameFromFilename(FilenamePrefix.c_str());
    104     LOG(0, "Chemical formula is " << (*iter)->getFormula());
     100    molecule * const mol = World::getInstance().getMolecule(MoleculeByOrder(-1));
     101    mol->SetNameFromFilename(FilenamePrefix.c_str());
     102    LOG(0, "Chemical formula is " << mol->getFormula());
    105103  }
    106104  return Action::success;

  • src/Actions/WorldAction/RepeatBoxAction.cpp

    rdf5b8c r2affd1  
    4040#include "CodePatterns/Log.hpp"
    4141#include "molecule.hpp"
    42 #include "MoleculeListClass.hpp"
    4342#include "LinearAlgebra/Vector.hpp"
    4443#include "LinearAlgebra/RealSpaceMatrix.hpp"
    … …  
    8685  // add molecules in each repeated domain part
    8786  std::vector<Vector> vectors;
    88   MoleculeListClass *molecules = World::getInstance().getMolecules();
    8987  for (n[0] = 0; n[0] < Repeater[0]; n[0]++) {
    9088    y[0] = n[0];
    … …  
    9997          LOG(2, "DEBUG: Current mol is " << mol->name << "." << endl);
    10098          molecule * const newmol = mol->CopyMolecule();
    101           // TODO: remove this when World does not have MoleculeListClass anymore.
    102           molecules->insert(newmol);
    10399          x = y;
    104100          x *= M;

  • src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp

    rdf5b8c r2affd1  
    4747#include "Element/periodentafel.hpp"
    4848#include "molecule.hpp"
    49 #include "MoleculeListClass.hpp"
    5049#include "World.hpp"
    5150

  • src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.hpp

    rdf5b8c r2affd1  
    1919class element;
    2020class molecule;
    21 class MoleculeListClass;
    2221class Vector;
    2322

  • src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp

    rdf5b8c r2affd1  
    5050#include "LinkedCell/PointCloudAdaptor.hpp"
    5151#include "molecule.hpp"
    52 #include "MoleculeListClass.hpp"
    5352#include "Tesselation/boundary.hpp"
    5453#include "Tesselation/tesselation.hpp"

  • src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp

    rdf5b8c r2affd1  
    2020class LinkedCell_deprecated;
    2121class molecule;
    22 class MoleculeListClass;
    2322class periodentafel;
    2423class Tesselation;

  • src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp

    rdf5b8c r2affd1  
    5050#include "Element/periodentafel.hpp"
    5151#include "molecule.hpp"
    52 #include "MoleculeListClass.hpp"
    5352#include "World.hpp"
    5453

  • src/Analysis/unittests/AnalysisPairCorrelationUnitTest.hpp

    rdf5b8c r2affd1  
    1919class element;
    2020class molecule;
    21 class MoleculeListClass;
    2221class Vector;
    2322

  • src/Fragmentation/Exporters/ExportGraph.cpp

    rdf5b8c r2affd1  
    4848#include "Graph/ListOfLocalAtoms.hpp"
    4949#include "molecule.hpp"
    50 #include "MoleculeListClass.hpp"
    5150#include "World.hpp"
    5251

  • src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp

    rdf5b8c r2affd1  
    4747#include "Graph/ListOfLocalAtoms.hpp"
    4848#include "molecule.hpp"
    49 #include "MoleculeListClass.hpp"
    5049#include "Parser/FormatParserStorage.hpp"
    5150#include "World.hpp"

  • src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp

    rdf5b8c r2affd1  
    1919#include "Fragmentation/HydrogenSaturation_enum.hpp"
    2020#include "Fragmentation/Exporters/ExportGraph.hpp"
    21 #include "MoleculeListClass.hpp"
    2221
    2322/** ExportGraph_ToJobs implements an ExportGraph by sending the created

  • src/Graph/ConnectedSubgraph.cpp

    rdf5b8c r2affd1  
    4444#include "CodePatterns/Verbose.hpp"
    4545#include "molecule.hpp"
    46 #include "MoleculeListClass.hpp"
    4746#include "World.hpp"
    4847
    … …  
    5756  molecule *mol = World::getInstance().createMolecule();
    5857  mol->ActiveFlag = true;
    59   // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
    60   World::getInstance().getMolecules()->insert(mol);
    6158
    6259  ASSERT(!empty(),

  • src/Graph/DepthFirstSearchAnalysis.cpp

    rdf5b8c r2affd1  
    5252#include "molecule.hpp"
    5353#include "MoleculeLeafClass.hpp"
    54 #include "MoleculeListClass.hpp"
    5554#include "World.hpp"
    5655
    … …  
    434433      World::getInstance().getMoleculeIter() != World::getInstance().moleculeEnd();
    435434      iter = World::getInstance().getMoleculeIter()) {
    436     // TODO: remove when deprecated MoleculeListClass is gone
    437     World::getInstance().getMolecules()->erase(*iter);
    438435    World::getInstance().destroyMolecule(*iter);
    439436  }

  • src/Parser/MpqcParser.cpp

    rdf5b8c r2affd1  
    5454#include "LinearAlgebra/Vector.hpp"
    5555#include "molecule.hpp"
    56 #include "MoleculeListClass.hpp"
    5756#include "Parser/Exceptions.hpp"
    5857#include "World.hpp"
    … …  
    101100  molecule *newmol = World::getInstance().createMolecule();
    102101  newmol->ActiveFlag = true;
    103   // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
    104   World::getInstance().getMolecules()->insert(newmol);
    105102  while (file->good()) {
    106103    file->getline(line, MAXSTRINGSIZE-1);

  • src/Parser/PcpParser.cpp

    rdf5b8c r2affd1  
    4848#include "LinearAlgebra/RealSpaceMatrix.hpp"
    4949#include "molecule.hpp"
    50 #include "MoleculeListClass.hpp"
    5150#include "PcpParser.hpp"
    5251#include "Parser/ConfigFileBuffer.hpp"
    … …  
    381380  molecule *mol = World::getInstance().createMolecule();
    382381  mol->ActiveFlag = true;
    383   // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
    384   World::getInstance().getMolecules()->insert(mol);
    385382  LoadMolecule(mol, FileBuffer, World::getInstance().getPeriode(), FastParsing);
    386383

  • src/Parser/PdbParser.cpp

    rdf5b8c r2affd1  
    4747#include "Element/periodentafel.hpp"
    4848#include "molecule.hpp"
    49 #include "MoleculeListClass.hpp"
    5049#include "Parser/PdbParser.hpp"
    5150#include "World.hpp"
    … …  
    140139  newmol->ActiveFlag = true;
    141140  unsigned int step = 0;
    142   // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
    143   World::getInstance().getMolecules()->insert(newmol);
    144141  while (NotEndOfFile) {
    145142    bool NotEndOfTimestep = true;

  • src/Parser/Psi3Parser.cpp

    rdf5b8c r2affd1  
    5252#include "LinearAlgebra/Vector.hpp"
    5353#include "molecule.hpp"
    54 #include "MoleculeListClass.hpp"
    5554#include "World.hpp"
    5655
    … …  
    9392  molecule *newmol = World::getInstance().createMolecule();
    9493  newmol->ActiveFlag = true;
    95   // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
    96   World::getInstance().getMolecules()->insert(newmol);
    9794  while (file->good()) {
    9895    file->getline(line, MAXSTRINGSIZE-1);

  • src/Parser/TremoloParser.cpp

    rdf5b8c r2affd1  
    5151#include "LinearAlgebra/RealSpaceMatrix.hpp"
    5252#include "molecule.hpp"
    53 #include "MoleculeListClass.hpp"
    5453#include "World.hpp"
    5554#include "WorldTime.hpp"
    … …  
    142141  molecule *newmol = World::getInstance().createMolecule();
    143142  newmol->ActiveFlag = true;
    144   // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
    145   World::getInstance().getMolecules()->insert(newmol);
    146143  while (file->good()) {
    147144    std::getline(*file, line, '\n');

  • src/Parser/XmlParser.cpp

    rdf5b8c r2affd1  
    4949#include "Element/periodentafel.hpp"
    5050#include "molecule.hpp"
    51 #include "MoleculeListClass.hpp"
    5251#include "World.hpp"
    5352
    … …  
    133132  molecule * const newmol = World::getInstance().createMolecule();
    134133  newmol->ActiveFlag = true;
    135   // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
    136   World::getInstance().getMolecules()->insert(newmol);
    137134
    138135  // load file into xml tree

  • src/Parser/XyzParser.cpp

    rdf5b8c r2affd1  
    4848#include "Element/periodentafel.hpp"
    4949#include "molecule.hpp"
    50 #include "MoleculeListClass.hpp"
    5150#include "World.hpp"
    5251
    … …  
    8988  newmol = World::getInstance().createMolecule();
    9089  newmol->ActiveFlag = true;
    91   // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
    92   World::getInstance().getMolecules()->insert(newmol);
    9390
    9491  // the first line tells number of atoms,

  • src/UIElements/TextUI/TextWindow.cpp

    rdf5b8c r2affd1  
    5050#include "Actions/ActionQueue.hpp"
    5151#include "Actions/ActionTrait.hpp"
     52#include "Element/element.hpp"
     53#include "Element/periodentafel.hpp"
     54#include "molecule.hpp"
    5255#include "Parser/ChangeTracker.hpp"
    5356#include "Views/StreamStringView.hpp"
    … …  
    5861#include "CodePatterns/Log.hpp"
    5962#include "CodePatterns/Verbose.hpp"
    60 
    61 // needed due to Enumerate()
    62 #include "MoleculeListClass.hpp"
    6363
    6464#include <iostream>
    … …  
    7676  main_menu->reserveShortcut('q', "quit");
    7777
    78   moleculeView = new StreamStringView(boost::bind(&MoleculeListClass::Enumerate,World::getInstance().getMolecules(),_1));
     78  moleculeView = new StreamStringView(boost::bind(&TextWindow::Enumerate,this,_1));
    7979  new DisplayMenuItem(main_menu->getMenuInstance(),moleculeView,"Molecule List");
    8080
    … …  
    9999}
    100100
     101void TextWindow::Enumerate(std::ostream *out)
     102{
     103  periodentafel *periode = World::getInstance().getPeriode();
     104  std::vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
     105  std::map<atomicNumber_t,unsigned int> counts;
     106  double size=0;
     107  Vector Origin;
     108
     109  // header
     110  (*out) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
     111  (*out) << "-----------------------------------------------" << endl;
     112  if (allmolecules.size() == 0)
     113    (*out) << "\tNone" << endl;
     114  else {
     115    Origin.Zero();
     116    for (std::vector<molecule *>::const_iterator ListRunner = allmolecules.begin();
     117        ListRunner != allmolecules.end(); ListRunner++) {
     118      // count atoms per element and determine size of bounding sphere
     119      size=0.;
     120      const molecule *MolRunner = *ListRunner;
     121      for (molecule::const_iterator iter = MolRunner->begin(); iter != MolRunner->end(); ++iter) {
     122        counts[(*iter)->getType()->getAtomicNumber()]++;
     123        if ((*iter)->DistanceSquared(Origin) > size)
     124          size = (*iter)->DistanceSquared(Origin);
     125      }
     126      // output Index, Name, number of atoms, chemical formula
     127      (*out) << (MolRunner->ActiveFlag ? "*" : " ") << MolRunner->IndexNr << "\t" << MolRunner->name << "\t\t" << MolRunner->getAtomCount() << "\t";
     128
     129      std::map<atomicNumber_t,unsigned int>::reverse_iterator iter;
     130      for(iter=counts.rbegin(); iter!=counts.rend();++iter){
     131        atomicNumber_t Z =(*iter).first;
     132        (*out) << periode->FindElement(Z)->getSymbol() << (*iter).second;
     133      }
     134      // Center and size
     135      Vector Center = MolRunner->DetermineCenterOfAll();
     136      (*out) << "\t" << Center << "\t" << sqrt(size) << endl;
     137    }
     138  }
     139}
     140
    101141TextWindow::~TextWindow()
    102142{

  • src/UIElements/TextUI/TextWindow.hpp

    rdf5b8c r2affd1  
    4141  TextMenu<TxMenu> *main_menu;
    4242
     43  /** Helper function to enumerate all molecules in the World.
     44   *
     45   * \param out output stream to write to
     46   */
     47  void Enumerate(std::ostream *out);
     48
    4349  MoleCuilder::Action *quitAction;
    4450  // all views that are contained in the main Menu

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

    rdf5b8c r2affd1  
    6262#include "Formula.hpp"
    6363#include "molecule.hpp"
    64 #include "MoleculeListClass.hpp"
    6564
    6665using namespace std;

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

    rdf5b8c r2affd1  
    3232
    3333class molecule;
    34 class MoleculeListClass;
    3534class QtMoleculeItem;
    3635class QtMoleculeListView;

  • src/World.cpp

    rdf5b8c r2affd1  
    6565#include "LinkedCell/PointCloudAdaptor.hpp"
    6666#include "molecule.hpp"
    67 #include "MoleculeListClass.hpp"
    6867#include "Thermostats/ThermoStatContainer.hpp"
    6968#include "WorldTime.hpp"
    … …  
    180179
    181180int World::numMolecules() const {
    182   return molecules_deprecated->ListOfMolecules.size();
     181  return molecules.size();
    183182}
    184183
    … …  
    355354    NOTIFY(MoleculeRemoved);
    356355  }
    357   // TODO: removed when depcreated MoleculeListClass is gone
    358   molecules_deprecated->erase(mol);
    359356  if (isMoleculeSelected(id)) {
    360357    selectedMolecules.erase(id);
    … …  
    10371034    molecules(this),
    10381035    selectedMolecules(this),
    1039     moleculeIdPool(0, 20,100),
    1040     molecules_deprecated(new MoleculeListClass(this))
     1036    moleculeIdPool(0, 20,100)
    10411037{
    10421038  cell_size = new Box;
    … …  
    10581054  delete LCcontroller;
    10591055  delete cell_size;
    1060   delete molecules_deprecated;
    10611056  MoleculeSet::iterator molIter;
    10621057  for(molIter=molecules.begin();molIter!=molecules.end();++molIter){
    … …  
    10881083
    10891084CONSTRUCT_OBSERVEDCONTAINER(World::MoleculeSTLSet, UnobservedIterator<World::MoleculeSTLSet> )
    1090 
    1091 /******************************* deprecated Legacy Stuff ***********************/
    1092 
    1093 MoleculeListClass *&World::getMolecules() {
    1094   return molecules_deprecated;
    1095 }

  • src/World.hpp

    rdf5b8c r2affd1  
    5252class MoleculeDescriptor;
    5353class MoleculeDescriptor_impl;
    54 class MoleculeListClass;
    5554class periodentafel;
    5655class ThermoStatContainer;
    … …  
    621620  virtual ~World();
    622621
    623   /*****
    624    * some legacy stuff that is include for now but will be removed later
    625    *****/
    626 public:
    627   MoleculeListClass *&getMolecules();
    628 
    629 private:
    630   MoleculeListClass *molecules_deprecated;
    631622};
    632623

  • src/molecule.hpp

    rdf5b8c r2affd1  
    5656class molecule;
    5757class MoleculeLeafClass;
    58 class MoleculeListClass;
    5958class MoleculeUnittest;
    6059class RealSpaceMatrix;
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