Changeset 21585f for src/Parser

Timestamp:

Aug 28, 2010, 12:57:56 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:

af2c424

Parents:

bb6193

git-author:

Frederik Heber <heber@…> (08/27/10 12:30:25)

git-committer:

Frederik Heber <heber@…> (08/28/10 00:57:56)

Message:

Added getter/setter for PdbParser::atomIdMap().

Location:

src/Parser

Files:

• PdbParser.cpp (modified) (3 diffs)
• PdbParser.hpp (modified) (1 diff)

src/Parser/PdbParser.cpp

@@ -138 +138 @@
       }
       saveLine(file, *atomIt, name, AtomNo, MolNo);
-      atomIdMap.insert( pair<int, int>((*atomIt)->getId(), AtomNo) );
+      setAtomId((*atomIt)->getId(), AtomNo);
       AtomNo++;
     }
@@ -196 +196 @@
   if (!currentAtom->ListOfBonds.empty()) {
     *file << "CONECT";
+    *file << setw(5) << getAtomId(currentAtom->getId());
     int MaxNo = 0;
     for(BondList::iterator currentBond = currentAtom->ListOfBonds.begin(); currentBond != currentAtom->ListOfBonds.end(); ++currentBond) {
       if (MaxNo < MaxnumberOfNeighbors) {
-        ASSERT(atomIdMap.find((*currentBond)->GetOtherAtom(currentAtom)->getId()) != atomIdMap.end(), "Id of atom not stored in PdbParser::atomIdMap.");
-        *file << setw(5) << atomIdMap[(*currentBond)->GetOtherAtom(currentAtom)->getId()];
+        *file << setw(5) << getAtomId((*currentBond)->GetOtherAtom(currentAtom)->getId());
       }
       MaxNo++;
@@ -206 +206 @@
     *file << endl;
   }
+}
+
+
+/** Retrieves a value from PdbParser::atomIdMap.
+ * \param atomid key
+ * \return value
+ */
+int PdbParser::getAtomId(int atomid) const
+{
+  ASSERT(atomIdMap.find(atomid) != atomIdMap.end(), "PdbParser::getAtomId: atomid not present in Map.");
+  return (atomIdMap.find(atomid)->second);
+}
+
+/** Sets an entry in PdbParser::atomIdMap.
+ * \param localatomid key
+ * \param atomid value
+ * \return true - key not present, false - value present
+ */
+void PdbParser::setAtomId(int localatomid, int atomid)
+{
+  pair<std::map<int,int>::iterator, bool > inserter;
+  inserter = atomIdMap.insert( pair<int, int>(localatomid, atomid) );
+  ASSERT(inserter.second, "PdbParser::setAtomId: atomId already present in Map.");
 }
 

src/Parser/PdbParser.hpp

@@ -76 +76 @@
   void writeNeighbors(std::ostream* file, int numberOfNeighbors, atom* currentAtom);
   void saveLine(ostream* file, const atom* currentAtom, const char *name, const int AtomNo, const int ResdueNo);
-;
+  int getAtomId(int atomid) const;
+  void setAtomId(int localatomid, int atomid);
 
   /**