Changeset 1f693d for src


Ignore:
Timestamp:
Apr 17, 2013, 6:56:54 PM (12 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, 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:
2d5137
Parents:
88ada9
git-author:
Frederik Heber <heber@…> (03/19/13 08:40:28)
git-committer:
Frederik Heber <heber@…> (04/17/13 18:56:54)
Message:

Wrapped Bond::BondDegree in getter.

Location:
src
Files:
16 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/GraphAction/CreateAdjacencyAction.cpp

    r88ada9 r1f693d  
    9696        BondInfo.leftatom = CurrentBond->leftatom->getId();
    9797        BondInfo.rightatom = CurrentBond->rightatom->getId();
    98         BondInfo.degree = CurrentBond->BondDegree;
     98        BondInfo.degree = CurrentBond->getDegree();
    9999        bonds.push_back(BondInfo);
    100100      }
    … …  
    139139        "GraphCreateAdjacencyAction::performUndo() - "+toString(iter->rightatom)+" missing.");
    140140    bond::ptr CurrentBond = Walker->addBond(CurrentTime, OtherWalker);
    141     CurrentBond->BondDegree = iter->degree;
     141    CurrentBond->setDegree(iter->degree);
    142142  }
    143143  return Action::state_ptr(_state);

  • src/Actions/GraphAction/DestroyAdjacencyAction.cpp

    r88ada9 r1f693d  
    104104        BondInfo.leftatom = CurrentBond->leftatom->getId();
    105105        BondInfo.rightatom = CurrentBond->rightatom->getId();
    106         BondInfo.degree = CurrentBond->BondDegree;
     106        BondInfo.degree = CurrentBond->getDegree();
    107107        bonds.push_back(BondInfo);
    108108      }
    … …  
    131131        "GraphDestroyAdjacencyAction::performUndo() - "+toString(iter->rightatom)+" missing.");
    132132    bond::ptr CurrentBond = Walker->addBond(CurrentTime, OtherWalker);
    133     CurrentBond->BondDegree = iter->degree;
     133    CurrentBond->setDegree(iter->degree);
    134134  }
    135135  return Action::state_ptr(_state);

  • src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp

    r88ada9 r1f693d  
    7474          LOG(3, "DEBUG: Creating copy bond between original " << Binder->leftatom->getId()
    7575              << " and " << Binder->rightatom->getId() << ": " << *NewBond << ".");
    76           NewBond->BondDegree = Binder->BondDegree;
     76          NewBond->setDegree(Binder->getDegree());
    7777          NewBond->Cyclic = Binder->Cyclic;
    7878          NewBond->Type = Binder->Type;

  • src/Atom/atom_bondedparticle.cpp

    r88ada9 r1f693d  
    7979  for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); ++Runner) {
    8080    ost << **Runner << "\t";
    81     TotalDegree += (*Runner)->BondDegree;
     81    TotalDegree += (*Runner)->getDegree();
    8282  }
    8383  ost << " -- TotalDegree: " << TotalDegree;
    … …  
    130130bond::ptr BondedParticle::addBond(BondedParticle* Partner)
    131131{
    132   addBond(WorldTime::getTime(), Partner);
     132  return addBond(WorldTime::getTime(), Partner);
    133133}
    134134
    … …  
    383383    }
    384384    if ((CandidateBond != NULL)) {
    385       CandidateBond->BondDegree++;
     385      CandidateBond->setDegree(CandidateBond->getDegree()+1);
    386386      LOG(2, "Increased bond degree for bond " << *CandidateBond << ".");
    387387    } else {
    … …  
    405405        BondRunner != (*Runner).end();
    406406        ++BondRunner)
    407       (*BondRunner)->BondDegree = 1;
     407      (*BondRunner)->setDegree(1);
    408408};
    409409
    … …  
    419419      Runner != ListOfBonds.end();
    420420      (++Runner))
    421     NoBonds += (*Runner)->BondDegree;
     421    NoBonds += (*Runner)->getDegree();
    422422  return NoBonds;
    423423};

  • src/Bond/BondInfo.cpp

    r88ada9 r1f693d  
    5252  leftid(_bond->leftatom->getId()),
    5353  rightid(_bond->rightatom->getId()),
    54   degree(_bond->BondDegree)
     54  degree(_bond->getDegree())
    5555{}
    5656
    … …  
    7777  LOG(3, "DEBUG: Re-creating bond " << leftid << "<->" << rightid << ".");
    7878  bond::ptr const _bond = leftatom->addBond(WorldTime::getTime(), rightatom);
    79   _bond->BondDegree = degree;
     79  _bond->setDegree(degree);
    8080  return true;
    8181}

  • src/Bond/bond.cpp

    r88ada9 r1f693d  
    9090ostream & operator << (ostream &ost, const bond &b)
    9191{
    92   ost << "[" << b.leftatom->getName() << " <" << b.BondDegree << "(H" << b.HydrogenBond << ")>" << b.rightatom->getName() << "]";
     92  ost << "[" << b.leftatom->getName() << " <" << b.getDegree() << "(H" << b.HydrogenBond << ")>" << b.rightatom->getName() << "]";
    9393  return ost;
    9494};
    … …  
    156156    rightatom = NULL;
    157157}
     158
     159void bond::setDegree(const int _degree)
     160{
     161  OBSERVE;
     162  BondDegree = _degree;
     163  NOTIFY(DegreeChanged);
     164}

  • src/Bond/bond.hpp

    r88ada9 r1f693d  
    4747  atom *rightatom;  //!< second bond partner
    4848  int HydrogenBond;  //!< Number of hydrogen atoms in the bond
    49   int BondDegree;    //!< single, double, triple, ... bond
    5049
    5150  atom * GetOtherAtom(const ParticleInfo * const Atom) const;
    … …  
    6059  ~bond();
    6160
     61  /** Getter for bond degree.
     62   *
     63   * \return degree
     64   */
     65  int getDegree() const { return BondDegree; }
     66
     67  /** Getter for bond degree.
     68   *
     69   * \param _degree new degree to set
     70   */
     71  void setDegree(const int _degree);
     72
     73private:
     74  int BondDegree;    //!< single, double, triple, ... bond
     75
    6276private:
    6377  //!> grant atom_bondedparticle access to unregister function

  • src/Bond/bond_observable.hpp

    r88ada9 r1f693d  
    2828  enum NotificationType {
    2929    BondRemoved,          // bond is about to be removed
     30    DegreeChanged,        // bond degree is different
    3031    NotificationType_MAX  // denotes the maximum of available notification types
    3132  };

  • src/Fragmentation/Exporters/ExportGraph.cpp

    r88ada9 r1f693d  
    227227            std::stringstream output;
    228228//            output << "ACCEPT: Adding Bond: "
    229             output << Leaf->AddBond((*iter), SonList[OtherFather->getNr()], (*BondRunner)->BondDegree);
     229            output << Leaf->AddBond((*iter), SonList[OtherFather->getNr()], (*BondRunner)->getDegree());
    230230//            LOG(3, output.str());
    231231            //NumBonds[(*iter)->getNr()]++;
    … …  
    244244            // just copy the atom if it's a hydrogen
    245245            atom * const OtherWalker = Leaf->AddCopyAtom(OtherFather);
    246             Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->BondDegree);
     246            Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->getDegree());
    247247          }
    248           //NumBonds[(*iter)->getNr()] += Binder->BondDegree;
     248          //NumBonds[(*iter)->getNr()] += Binder->getDegree();
    249249        }
    250250      }

  • src/Fragmentation/Exporters/SaturatedFragment.cpp

    r88ada9 r1f693d  
    130130////          std::stringstream output;
    131131////            output << "ACCEPT: Adding Bond: "
    132 //          output << Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->BondDegree);
     132//          output << Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->getDegree());
    133133////            LOG(3, output.str());
    134134//          //NumBonds[(*iter)->getNr()]++;
    … …  
    152152//          // just copy the atom if it's a hydrogen
    153153//          atom * const OtherWalker = Leaf->AddCopyAtom(OtherWalker);
    154 //          Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->BondDegree);
     154//          Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->getDegree());
    155155//        }
    156         //NumBonds[(*iter)->getNr()] += Binder->BondDegree;
     156        //NumBonds[(*iter)->getNr()] += Binder->getDegree();
    157157      }
    158158    }
    … …  
    266266  ASSERT(Origin->getType() != NULL,
    267267      "SaturatedFragment::AddHydrogenReplacementAtom() - element of Origin is not given.");
    268   BondRescale = Origin->getType()->getHBondDistance(TopBond->BondDegree-1);
     268  BondRescale = Origin->getType()->getHBondDistance(TopBond->getDegree()-1);
    269269  if (BondRescale == -1) {
    270     ELOG(1, "There is no typical hydrogen bond distance in replacing bond (" << Origin->getName() << "<->" << Replacement->getName() << ") of degree " << TopBond->BondDegree << "!");
     270    ELOG(1, "There is no typical hydrogen bond distance in replacing bond (" << Origin->getName() << "<->" << Replacement->getName() << ") of degree " << TopBond->getDegree() << "!");
    271271    return false;
    272272    BondRescale = bondlength;
    … …  
    277277
    278278  // discern single, double and triple bonds
    279   switch(TopBond->BondDegree) {
     279  switch(TopBond->getDegree()) {
    280280    case 1:
    281281      // check whether replacement has been an excluded hydrogen
    … …  
    343343      bondangle = Origin->getType()->getHBondAngle(1);
    344344      if (bondangle == -1) {
    345         ELOG(1, "There is no typical hydrogen bond angle in replacing bond (" << Origin->getName() << "<->" << Replacement->getName() << ") of degree " << TopBond->BondDegree << "!");
     345        ELOG(1, "There is no typical hydrogen bond angle in replacing bond (" << Origin->getName() << "<->" << Replacement->getName() << ") of degree " << TopBond->getDegree() << "!");
    346346        return false;
    347347        bondangle = 0;

  • src/Graph/BuildInducedSubgraph.cpp

    r88ada9 r1f693d  
    8686          if (ParentList.count(OtherAtom)) { // if otheratom is also a father of an atom on this molecule, create the bond
    8787            LOG(4, "INFO: Endpoints of Bond " << (*Runner) << " are both present: " << ParentList[(*iter)]->getName() << " and " << ParentList[OtherAtom]->getName() << ".");
    88             Son->AddBond(ParentList[(*iter)], ParentList[OtherAtom], (*Runner)->BondDegree);
     88            Son->AddBond(ParentList[(*iter)], ParentList[OtherAtom], (*Runner)->getDegree());
    8989          }
    9090        }

  • src/Parser/Psi3Parser.cpp

    r88ada9 r1f693d  
    269269  BOOST_FOREACH(atom *_atom, atoms) {
    270270    BOOST_FOREACH(bond::ptr _bond, _atom->getListOfBonds()) {
    271       degrees += 2*_bond->BondDegree;
     271      degrees += 2*_bond->getDegree();
    272272    }
    273273  }

  • src/Tesselation/boundary.cpp

    r88ada9 r1f693d  
    915915              if ((CopyAtoms[Binder->leftatom->getNr()] != NULL) && (CopyAtoms[Binder->rightatom->getNr()] != NULL)) {
    916916                LOG(3, "Adding Bond between " << *CopyAtoms[Binder->leftatom->getNr()] << " and " << *CopyAtoms[Binder->rightatom->getNr()]<< ".");
    917                 Filling->AddBond(CopyAtoms[Binder->leftatom->getNr()], CopyAtoms[Binder->rightatom->getNr()], Binder->BondDegree);
     917                Filling->AddBond(CopyAtoms[Binder->leftatom->getNr()], CopyAtoms[Binder->rightatom->getNr()], Binder->getDegree());
    918918              }
    919919            }

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

    r88ada9 r1f693d  
    177177#endif
    178178  if (publisher == static_cast<const Observable *>(&_bond)){
    179     delete this;
     179    switch (notification->getChannelNo()) {
     180    case BondObservable::BondRemoved:
     181      delete this;
     182      break;
     183    }
    180184  } else {
    181185    bool DoResetPosition = false;

  • src/molecule.cpp

    r88ada9 r1f693d  
    382382  // get typical bond length and store as scale factor for later
    383383  ASSERT(TopOrigin->getType() != NULL, "AddHydrogenReplacementAtom: element of TopOrigin is not given.");
    384   BondRescale = TopOrigin->getType()->getHBondDistance(TopBond->BondDegree-1);
     384  BondRescale = TopOrigin->getType()->getHBondDistance(TopBond->getDegree()-1);
    385385  if (BondRescale == -1) {
    386     ELOG(1, "There is no typical hydrogen bond distance in replacing bond (" << TopOrigin->getName() << "<->" << TopReplacement->getName() << ") of degree " << TopBond->BondDegree << "!");
     386    ELOG(1, "There is no typical hydrogen bond distance in replacing bond (" << TopOrigin->getName() << "<->" << TopReplacement->getName() << ") of degree " << TopBond->getDegree() << "!");
    387387    return false;
    388388    BondRescale = bondlength;
    … …  
    393393
    394394  // discern single, double and triple bonds
    395   switch(TopBond->BondDegree) {
     395  switch(TopBond->getDegree()) {
    396396    case 1:
    397397      FirstOtherAtom = World::getInstance().createAtom();    // new atom
    … …  
    471471      bondangle = TopOrigin->getType()->getHBondAngle(1);
    472472      if (bondangle == -1) {
    473         ELOG(1, "There is no typical hydrogen bond angle in replacing bond (" << TopOrigin->getName() << "<->" << TopReplacement->getName() << ") of degree " << TopBond->BondDegree << "!");
     473        ELOG(1, "There is no typical hydrogen bond angle in replacing bond (" << TopOrigin->getName() << "<->" << TopReplacement->getName() << ") of degree " << TopBond->getDegree() << "!");
    474474        return false;
    475475        bondangle = 0;
    … …  
    620620        atom * const RightAtom = FatherFinder[Binder->rightatom];
    621621
    622         bond::ptr const NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
     622        bond::ptr const NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->getDegree());
    623623        NewBond->Cyclic = Binder->Cyclic;
    624624        if (Binder->Cyclic)
    … …  
    676676          atom * const RightAtom = FatherFinder[Binder->rightatom];
    677677
    678           bond::ptr const NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
     678          bond::ptr const NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->getDegree());
    679679          NewBond->Cyclic = Binder->Cyclic;
    680680          if (Binder->Cyclic)

  • src/molecule_graph.cpp

    r88ada9 r1f693d  
    9999        if (OtherWalker != NULL) {
    100100          if (OtherWalker->getNr() > (*iter)->getNr())
    101             AddBond((*iter), OtherWalker, (*Runner)->BondDegree);
     101            AddBond((*iter), OtherWalker, (*Runner)->getDegree());
    102102        } else {
    103103          LOG(1, "OtherWalker = ListOfLocalAtoms[" << OtherAtom->getNr() << "] is NULL!");
    … …  
    192192bond::ptr molecule::CopyBond(atom *left, atom *right, bond::ptr CopyBond)
    193193{
    194   bond::ptr Binder = AddBond(left, right, CopyBond->BondDegree);
     194  bond::ptr Binder = AddBond(left, right, CopyBond->getDegree());
    195195  Binder->Cyclic = CopyBond->Cyclic;
    196196  Binder->Type = CopyBond->Type;
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