Changeset 4d2b33 for src/moleculelist.cpp

Timestamp:

Mar 27, 2012, 3:53:35 PM (13 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:

46c832

Parents:

955b91

git-author:

Frederik Heber <heber@…> (03/19/12 16:42:39)

git-committer:

Frederik Heber <heber@…> (03/27/12 15:53:35)

Message:

FIX: molecule does not need a periodentafel.

• removed periodentafel param from cstor.
• removed member variable elemente
• removed AddXyzFile which was sole user of elemente.
• removed depending functions in MoleculeListClass which were all remnants from old menu interface.

File:

• src/moleculelist.cpp (modified) (1 diff)

src/moleculelist.cpp

@@ -633 +633 @@
   return AtomNo;
 }
-
-/***********
- * Methods Moved here from the menus
- */
-
-void MoleculeListClass::createNewMolecule(periodentafel *periode) {
-  OBSERVE;
-  molecule *mol = NULL;
-  mol = World::getInstance().createMolecule();
-  insert(mol);
-};
-
-void MoleculeListClass::loadFromXYZ(periodentafel *periode){
-  molecule *mol = NULL;
-  Vector center;
-  char filename[MAXSTRINGSIZE];
-  std::cout << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
-  mol = World::getInstance().createMolecule();
-  do {
-    std::cout << "Enter file name: ";
-    cin >> filename;
-  } while (!mol->AddXYZFile(filename));
-  mol->SetNameFromFilename(filename);
-  // center at set box dimensions
-  mol->CenterEdge(&center);
-  RealSpaceMatrix domain;
-  for(int i =0;i<NDIM;++i)
-    domain.at(i,i) = center[i];
-  World::getInstance().setDomain(domain);
-  insert(mol);
-}
-
-void MoleculeListClass::setMoleculeFilename() {
-  char filename[MAXSTRINGSIZE];
-  int nr;
-  molecule *mol = NULL;
-  do {
-    std::cout << "Enter index of molecule: ";
-    cin >> nr;
-    mol = ReturnIndex(nr);
-  } while (mol == NULL);
-  std::cout << "Enter name: ";
-  cin >> filename;
-  mol->SetNameFromFilename(filename);
-}
-
-void MoleculeListClass::parseXYZIntoMolecule(){
-  char filename[MAXSTRINGSIZE];
-  int nr;
-  molecule *mol = NULL;
-  mol = NULL;
-  do {
-    std::cout << "Enter index of molecule: ";
-   cin >> nr;
-   mol = ReturnIndex(nr);
-  } while (mol == NULL);
-  std::cout << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
-  do {
-    std::cout << "Enter file name: ";
-   cin >> filename;
-  } while (!mol->AddXYZFile(filename));
-  mol->SetNameFromFilename(filename);
-};
-
-void MoleculeListClass::eraseMolecule(){
-  int nr;
-  molecule *mol = NULL;
-  std::cout << "Enter index of molecule: ";
-  cin >> nr;
-  for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
-    if (nr == (*ListRunner)->IndexNr) {
-      mol = *ListRunner;
-      ListOfMolecules.erase(ListRunner);
-      World::getInstance().destroyMolecule(mol);
-      break;
-    }
-};