Changeset 2affd1 for src/Actions/MoleculeAction

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/Actions/MoleculeAction

Files:

• BondFileAction.def (modified) (1 diff)
• ChangeNameAction.def (modified) (1 diff)
• LinearInterpolationofTrajectoriesAction.def (modified) (1 diff)
• LoadAction.cpp (modified) (4 diffs)
• RotateAroundSelfByAngleAction.def (modified) (1 diff)
• RotateToPrincipalAxisSystemAction.def (modified) (1 diff)
• SaveAdjacencyAction.def (modified) (1 diff)
• SaveBondsAction.def (modified) (1 diff)
• SaveTemperatureAction.def (modified) (1 diff)

src/Actions/MoleculeAction/BondFileAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
-class MoleculeListClass;
-
 #include "Parameters/Validators/DummyValidator.hpp"
 #include "Parameters/Validators/Specific/FilePresentValidator.hpp"

src/Actions/MoleculeAction/ChangeNameAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
-class MoleculeListClass;
-
 #include "Parameters/Validators/DummyValidator.hpp"
 

src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
-class MoleculeListClass;
-
 #include "Parameters/Validators/DummyValidator.hpp"
 #include "Parameters/Validators/GenericValidators.hpp"

src/Actions/MoleculeAction/LoadAction.cpp

@@ -38 +38 @@
 #include "CodePatterns/Verbose.hpp"
 #include "Descriptors/MoleculeIdDescriptor.hpp"
+#include "Descriptors/MoleculeOrderDescriptor.hpp"
 #include "Parser/Exceptions.hpp"
 #include "Parser/FormatParserInterface.hpp"
@@ -43 +44 @@
 #include "Parser/FormatParser_Parameters.hpp"
 #include "molecule.hpp"
-#include "MoleculeListClass.hpp"
 #include "World.hpp"
 
@@ -102 +102 @@
 
     // set file name of last molecule
-    MoleculeList::const_reverse_iterator iter = World::getInstance().getMolecules()->ListOfMolecules.rbegin();
-    (*iter)->SetNameFromFilename(FilenamePrefix.c_str());
-    LOG(0, "Chemical formula is " << (*iter)->getFormula());
+    molecule * const mol = World::getInstance().getMolecule(MoleculeByOrder(-1));
+    mol->SetNameFromFilename(FilenamePrefix.c_str());
+    LOG(0, "Chemical formula is " << mol->getFormula());
 
     return ActionState::ptr(
-        new MoleculeLoadState((*iter)->getId(),FilenamePrefix,FilenameSuffix,boost::shared_ptr<FormatParser_Parameters>(ParserParams),params)
+        new MoleculeLoadState(mol->getId(),FilenamePrefix,FilenameSuffix,boost::shared_ptr<FormatParser_Parameters>(ParserParams),params)
     );
   }
@@ -151 +151 @@
 
   // set file name of last molecule
-  MoleculeList::const_reverse_iterator iter = World::getInstance().getMolecules()->ListOfMolecules.rbegin();
-  (*iter)->SetNameFromFilename(state->FilenamePrefix.c_str());
-  (*iter)->setId(state->molId);
-  LOG(0, "Chemical formula is " << (*iter)->getFormula());
+  molecule * const mol = World::getInstance().getMolecule(MoleculeByOrder(-1));
+  mol->SetNameFromFilename(state->FilenamePrefix.c_str());
+  mol->setId(state->molId);
+  LOG(0, "Chemical formula is " << mol->getFormula());
 
   return ActionState::ptr(
-      new MoleculeLoadState((*iter)->getId(),state->FilenamePrefix,state->FilenameSuffix,boost::shared_ptr<FormatParser_Parameters>(ParserParams),params)
+      new MoleculeLoadState(mol->getId(),state->FilenamePrefix,state->FilenameSuffix,boost::shared_ptr<FormatParser_Parameters>(ParserParams),params)
   );
 }

src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
-class MoleculeListClass;
 class Vector;
 

src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def

@@ -9 +9 @@
 #include "Actions/Values.hpp"
 #include "LinearAlgebra/Vector.hpp"
-
-class MoleculeListClass;
 
 #include "Parameters/Validators/Specific/VectorNotZeroValidator.hpp"

src/Actions/MoleculeAction/SaveAdjacencyAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
-class MoleculeListClass;
-
 #include "Parameters/Validators/Ops_Validator.hpp"
 #include "Parameters/Validators/Specific/FilePresentValidator.hpp"

src/Actions/MoleculeAction/SaveBondsAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
-class MoleculeListClass;
-
 #include "Parameters/Validators/Ops_Validator.hpp"
 #include "Parameters/Validators/Specific/FilePresentValidator.hpp"

src/Actions/MoleculeAction/SaveTemperatureAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
-class MoleculeListClass;
-
 #include "Parameters/Validators/Ops_Validator.hpp"
 #include "Parameters/Validators/Specific/FilePresentValidator.hpp"