Changeset 4afa46 for src/Parser

Timestamp:

Mar 1, 2011, 10:16:38 AM (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:

9d37ac

Parents:

637358

git-author:

Frederik Heber <heber@…> (02/26/11 00:06:01)

git-committer:

Frederik Heber <heber@…> (03/01/11 10:16:38)

Message:

Added call to molecule::getAtomCount() to end of each parser's ::load().

• this ensures that atom::nr and name is up-to-date.

Location:

src/Parser

Files:

• MpqcParser.cpp (modified) (1 diff)
• PcpParser.cpp (modified) (1 diff)
• PdbParser.cpp (modified) (1 diff)
• TremoloParser.cpp (modified) (1 diff)
• XyzParser.cpp (modified) (1 diff)

src/Parser/MpqcParser.cpp

@@ -203 +203 @@
     }
   }
+  // refresh atom::nr and atom::name
+  newmol->getAtomCount();
 }
 

src/Parser/PcpParser.cpp

@@ -359 +359 @@
   World::getInstance().getMolecules()->insert(mol);
   LoadMolecule(mol, FileBuffer, World::getInstance().getPeriode(), FastParsing);
+
+  // refresh atom::nr and atom::name
+  mol->getAtomCount();
 
   // 4. dissect the molecule into connected subgraphs

src/Parser/PdbParser.cpp

@@ -159 +159 @@
   BOOST_FOREACH(atom *_atom, World::getInstance().getAllAtoms())
     LOG(4, "INFO: Atom " << _atom->getName() << " " << *dynamic_cast<AtomInfo *>(_atom) << ".");
+
+  // refresh atom::nr and atom::name
+  newmol->getAtomCount();
 }
 

src/Parser/TremoloParser.cpp

@@ -123 +123 @@
     }
   }
+  // refresh atom::nr and atom::name
+  newmol->getAtomCount();
 
   processNeighborInformation();

src/Parser/XyzParser.cpp

@@ -118 +118 @@
   BOOST_FOREACH(atom *_atom, World::getInstance().getAllAtoms())
     LOG(3, "INFO: Atom " << _atom->getName() << " " << *dynamic_cast<AtomInfo *>(_atom) << ".");
+
+  // refresh atom::nr and atom::name
+  newmol->getAtomCount();
 }