Changeset 8bf9c6 for src/Parser/PdbParser.cpp

Timestamp:

Feb 17, 2012, 3:24:17 PM (13 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:

812155

Parents:

2ad1ec

git-author:

Frederik Heber <heber@…> (01/06/12 13:11:42)

git-committer:

Frederik Heber <heber@…> (02/17/12 15:24:17)

Message:

All additionalAtomData maps now have const atomId_t as key.

File:

• src/Parser/PdbParser.cpp (modified) (3 diffs)

src/Parser/PdbParser.cpp

@@ -312 +312 @@
 {
   //LOG(3, "FormatParser< pdb >::AtomRemoved() - notified of atom " << id << "'s removal.");
-  std::map<size_t, PdbAtomInfoContainer>::iterator iter = additionalAtomData.find(id);
+  std::map<const atomId_t, PdbAtomInfoContainer>::iterator iter = additionalAtomData.find(id);
   // as we do not insert AtomData on AtomInserted, we cannot be assured of its presence
 //  ASSERT(iter != additionalAtomData.end(),
@@ -328 +328 @@
  * @return true - entry present, false - only for atom's father or no entry
  */
-bool FormatParser< pdb >::isPresentadditionalAtomData(unsigned int _id)
-{
-  return (additionalAtomData.find(_id) != additionalAtomData.end());
+bool FormatParser< pdb >::isPresentadditionalAtomData(const atomId_t _id) const
+{
+  std::map<const atomId_t, PdbAtomInfoContainer>::const_iterator iter = additionalAtomData.find(_id);
+  return (iter != additionalAtomData.end());
 }
 
@@ -480 +481 @@
   if (newAtom == NULL) {
     newAtom = World::getInstance().createAtom();
-    const unsigned int AtomID_global = newAtom->getId();
+    //const unsigned int AtomID_global = newAtom->getId();
     LOG(4, "INFO: No association to global id present, creating atom.");
   } else {