Changeset 2affd1 for src/Parser


Ignore:
Timestamp:
Feb 11, 2016, 8:07:11 AM (9 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:
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/Parser
Files:
7 edited

Legend:

Unmodified
Added
Removed

  • 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,
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