Changeset 73916f for src/Actions

Timestamp:

Dec 16, 2010, 5:32:22 PM (14 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:

fc5c3a

Parents:

512f85

git-author:

Frederik Heber <heber@…> (12/11/10 15:57:00)

git-committer:

Frederik Heber <heber@…> (12/16/10 17:32:22)

Message:

Extended FormatParser::save() to use vector<atom *> to save.

• This is needed to make the save functions also work on selected atoms or molecules only.
• Within ParserCommonUnitTest, ParserTremoloUnitTest we create the vector by calling World's getAllAtoms() (which would have been done before in the specialized save() functions).
• new functions in FormatParserStorage:
  • saveSelectedAtoms().
  • saveSelectedMolecules().
  • saveWorld().
• renamed ::get() and ::put() to ::load() and ::save() to have it more consistent with underlying FormatParser functions and also to avoid misinterpretation with all ::get...() functions.

Location:

src/Actions

Files:

• MoleculeAction/LoadAction.cpp (modified) (1 diff)
• MoleculeAction/SaveAction.cpp (modified) (1 diff)
• MoleculeAction/SaveAction.def (modified) (1 diff)
• WorldAction/InputAction.cpp (modified) (1 diff)

src/Actions/MoleculeAction/LoadAction.cpp

@@ -64 +64 @@
     boost::filesystem::ifstream input;
     input.open(params.filename);
-    FormatParserStorage::getInstance().get(input, FilenameSuffix);
+    FormatParserStorage::getInstance().load(input, FilenameSuffix);
     input.close();
 

src/Actions/MoleculeAction/SaveAction.cpp

@@ -60 +60 @@
   output.open(params.filename);
   if (!output.fail()) {
-    FormatParserStorage::getInstance().put(output, FilenameSuffix);
+    FormatParserStorage::getInstance().saveWorld(output, FilenameSuffix);
   } else {
     DoeLog(1) && (eLog() << Verbose(1) << "Could not open file " << params.filename << "." << endl);

src/Actions/MoleculeAction/SaveAction.def

@@ -30 +30 @@
 
 // finally the information stored in the ActionTrait specialization
-#define DESCRIPTION "save world as file of certain type"
+#define DESCRIPTION "save selected molecules as file of certain type"
 #define SHORTFORM "s"

src/Actions/WorldAction/InputAction.cpp

@@ -71 +71 @@
     // parse the file
     test.open(params.filename);
-    FormatParserStorage::getInstance().get(test, FilenameSuffix);
+    FormatParserStorage::getInstance().load(test, FilenameSuffix);
     test.close();