Changeset c0e28c for src/Parser/TremoloParser.cpp

Timestamp:

Jan 6, 2012, 2:02:08 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, Candidate_v1.7.0, 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:

d08ab3

Parents:

fbbcde

git-author:

Frederik Heber <heber@…> (01/04/12 18:34:22)

git-committer:

Frederik Heber <heber@…> (01/06/12 14:02:08)

Message:

FIX: One could not load another pdb file due to local ids messing up.

• We enhanced FormatParser_common now contains two maps to go from local to global and back again. Thi is necessary, as ids in a file only make sense within that file. We added the following functions: resetIdAssociations(), associateLocaltoGlobalId(), getGlobalId(), getLocalId().
• adapted TremoloParser and PdbParser because they are the only formats that also contain bond information and where the associations are needed to translate the local connections into global ones.
• removed SerialSet entirely from PdbParser, is replaced by new construct, in similar manner AtomIdMap for TremoloParser.
• TEST: Added regression tests for all Parser to check for loading twice the same file.

File:

• src/Parser/TremoloParser.cpp (modified) (5 diffs)

src/Parser/TremoloParser.cpp

@@ -103 +103 @@
   usedFields.clear();
   additionalAtomData.clear();
-  atomIdMap.clear();
   knownKeys.clear();
 }
@@ -116 +115 @@
   string::size_type location;
 
-  // reset atomIdMap, for we now get new serials
-  atomIdMap.clear();
+  // reset the id maps
+  resetIdAssociations();
+
   LOG(1, "INFO: Clearing usedFields.");
   usedFields.clear();
@@ -444 +444 @@
         ASSERT(tok_iter != tokens.end(), "FormatParser< tremolo >::readAtomDataLine() - no value for "+keyName+"!");
         LOG(4, "INFO: Parsing key " << keyName << " with next token " << *tok_iter);
-        atomIdMap[toInt(*tok_iter)] = atomid;
+        associateLocaltoGlobalId(toInt(*tok_iter), atomid);
         tok_iter++;
         break;
@@ -525 +525 @@
         neighbor != currentInfo->second.neighbors.end(); neighbor++
       ) {
-//        LOG(1, "INFO: Creating bond between ("
-//            << currentInfo->first
-//            << ") and ("
-//            << atomIdMap[*neighbor] << "|" << *neighbor << ")");
+        LOG(3, "INFO: Creating bond between ("
+            << currentInfo->first
+            << ") and ("
+            << getGlobalId(*neighbor) << "|" << *neighbor << ")");
+        ASSERT(getGlobalId(*neighbor) != -1,
+            "FormatParser< tremolo >::processNeighborInformation() - global id to local id "
+            +toString(*neighbor)+" is unknown.");
         World::getInstance().getAtom(AtomById(currentInfo->first))
-            ->addBond(WorldTime::getTime(), World::getInstance().getAtom(AtomById(atomIdMap[*neighbor])));
+            ->addBond(WorldTime::getTime(), World::getInstance().getAtom(AtomById(getGlobalId(*neighbor))));
       }
       currentInfo->second.neighbors_processed = true;
@@ -558 +561 @@
 
   line >> id;
-  result << atomIdMap[id];
+  result << getGlobalId(id);
   while (line.good()) {
     line >> separator >> id;
-    result << separator << atomIdMap[id];
+    result << separator << getGlobalId(id);
   }