Changeset 7a51be for src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp

Timestamp:

Feb 11, 2011, 9:37:26 PM (15 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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

f649de

Parents:

170ba6

Message:

new function FormatParserStorage::get to obtain specialized FormatParser instance.

• used in FillVoidWithMoleculeAction and FillWithMoleculeAction.
• both Actions also now use MoleculeByOrder descriptor to obtain last molecule.
• FillBoxWithMolecule() now returns void.
• implemented FillVoidWithMoleculeAction::performUndo().
• TEST: Filling/FillWithMolecule - added undo test.
• TESTFIX: Filling/FillVoidWithMolecule - due to loading of filler molecule with parser, water.data had to be adapted in its ATOMDATA line to match test.data. Otherwise, resulting file will have non-matching ATOMDATA although being otherwise consistent. (This is a workaround to ticket #141).

File:

• src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) (2 diffs)

src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp

@@ -23 +23 @@
 #include "bondgraph.hpp"
 #include "boundary.hpp"
+#include "CodePatterns/Verbose.hpp"
 #include "config.hpp"
+#include "Descriptors/MoleculeIdDescriptor.hpp"
+#include "Descriptors/MoleculeOrderDescriptor.hpp"
 #include "molecule.hpp"
-#include "CodePatterns/Verbose.hpp"
+#include "Parser/FormatParserStorage.hpp"
 #include "World.hpp"
 
-#include "Descriptors/MoleculeIdDescriptor.hpp"
-#include "Parser/MpqcParser.hpp"
-#include "Parser/PcpParser.hpp"
-#include "Parser/PdbParser.hpp"
-#include "Parser/TremoloParser.hpp"
-#include "Parser/XyzParser.hpp"
-#include "Parser/FormatParserStorage.hpp"
 
 #include <algorithm>
@@ -70 +66 @@
   ifstream input;
   input.open(params.fillername.string().c_str());
-  switch (FormatParserStorage::getInstance().getTypeFromSuffix(FilenameSuffix)) {
-    case mpqc:
-      {
-        MpqcParser mpqcparser;
-        mpqcparser.load(&input);
-        break;
-      }
-    case pcp:
-      {
-        PcpParser pcpparser;
-        pcpparser.load(&input);
-        break;
-      }
-    case pdb:
-      {
-        PdbParser pdbparser;
-        pdbparser.load(&input);
-        break;
-      }
-    case tremolo:
-      {
-        TremoloParser tremoloparser;
-        tremoloparser.load(&input);
-        break;
-      }
-    case xyz:
-      {
-        XyzParser xyzparser;
-        xyzparser.load(&input);
-        break;
-      }
-    default:
-      DoeLog(0) && (eLog()<< Verbose(0) << "Could not parse filler molecule from " << params.fillername << "." << endl);
-      break;
-  }
+  ParserTypes type = FormatParserStorage::getInstance().getTypeFromSuffix(FilenameSuffix);
+  FormatParser &parser = FormatParserStorage::getInstance().get(type);
+  parser.load(&input);
 
   // search the filler molecule that has been just parsed
-  molecule *filler = NULL;
-  for (World::MoleculeIterator iter = World::getInstance().getMoleculeIter();
-      iter != World::getInstance().moleculeEnd();
-      ++iter)
-    filler = *iter; // get last molecule
+  molecule *filler = World::getInstance().getMolecule(MoleculeByOrder(-1)); // get last molecule
   filler->SetNameFromFilename(params.fillername.string().c_str());
   World::getInstance().getConfig()->BG->ConstructBondGraph(filler);