Changeset 4c1230

Timestamp:

Dec 6, 2010, 8:47:33 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:

031e2c6

Parents:

a564be

Message:

FIX: PdbParser::writeNeighbors() uses getAtomId not getSerial.

• additionalAtomData is as of now not used for storing. Hence, we first fix this. Now, the set id in PdbParser::save is also used for the neighbor connectivity.

File:

• src/Parser/PdbParser.cpp (modified) (2 diffs)

src/Parser/PdbParser.cpp

@@ -235 +235 @@
  */
 void PdbParser::writeNeighbors(ostream* file, int MaxnumberOfNeighbors, atom* currentAtom) {
+  int MaxNo = MaxnumberOfNeighbors;
   if (!currentAtom->ListOfBonds.empty()) {
-    *file << "CONECT";
-    *file << setw(5) << getSerial(currentAtom->getId());
-    int MaxNo = 0;
     for(BondList::iterator currentBond = currentAtom->ListOfBonds.begin(); currentBond != currentAtom->ListOfBonds.end(); ++currentBond) {
-      if (MaxNo < MaxnumberOfNeighbors) {
-        *file << setw(5) << getSerial((*currentBond)->GetOtherAtom(currentAtom)->getId());
+      if (MaxNo >= MaxnumberOfNeighbors) {
+        *file << "CONECT";
+        *file << setw(5) << getAtomId(currentAtom->getId());
+        MaxNo = 0;
       }
+      *file << setw(5) << getAtomId((*currentBond)->GetOtherAtom(currentAtom)->getId());
       MaxNo++;
+      if (MaxNo == MaxnumberOfNeighbors)
+        *file << "\n";
     }
-    *file << endl;
+    if (MaxNo != MaxnumberOfNeighbors)
+      *file << "\n";
   }
 }
@@ -282 +286 @@
 {
   pair<std::map<size_t,size_t>::iterator, bool > inserter;
+  DoLog(1) && (Log() << Verbose(1) << "PdbParser::setAtomId() - Inserting ("
+      << localatomid << " -> " << atomid << ")." << std::endl);
   inserter = atomIdMap.insert( make_pair(localatomid, atomid) );
   ASSERT(inserter.second, "PdbParser::setAtomId: atomId already present in Map.");