Changeset 6bc86c for src

Timestamp:

Oct 10, 2011, 2:27:05 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:

e611dc

Parents:

38f991

git-author:

Frederik Heber <heber@…> (09/05/11 17:24:31)

git-committer:

Frederik Heber <heber@…> (10/10/11 14:27:05)

Message:

Implemented specific AtomRemoved(),AtomInserted() for Pdb and Tremolo parsers.

• each remove information from their ..AtomInfoContainers, if present.

Location:

src/Parser

Files:

• PdbParser.cpp (modified) (2 diffs)
• PdbParser.hpp (modified) (1 diff)
• TremoloParser.cpp (modified) (1 diff)
• TremoloParser.hpp (modified) (1 diff)

src/Parser/PdbParser.cpp

@@ -285 +285 @@
 }
 
+/** Add default info, when new atom is added to World.
+ *
+ * @param id of atom
+ */
+void PdbParser::AtomInserted(atomId_t id)
+{
+  //LOG(3, "PdbParser::AtomInserted() - notified of atom " << id << "'s insertion.");
+  ASSERT(!isPresentadditionalAtomData(id),
+      "PdbParser::AtomInserted() - additionalAtomData already present for newly added atom "
+      +toString(id)+".");
+  // don't insert here as this is our check whether we are in the first time step
+  //additionalAtomData.insert( std::make_pair(id, defaultAdditionalData) );
+  //SerialSet.insert(id);
+}
+
+/** Remove additional AtomData info, when atom has been removed from World.
+ *
+ * @param id of atom
+ */
+void PdbParser::AtomRemoved(atomId_t id)
+{
+  //LOG(3, "PdbParser::AtomRemoved() - notified of atom " << id << "'s removal.");
+  std::map<size_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(),
+//      "PdbParser::AtomRemoved() - additionalAtomData is not present for atom "
+//      +toString(id)+" to remove.");
+  if (iter != additionalAtomData.end()) {
+    ConvertTo<size_t> toSize_t;
+    SerialSet.erase(toSize_t((iter->second).get<std::string>(PdbKey::serial)));
+    additionalAtomData.erase(iter);
+  }
+}
+
+
 /** Checks whether there is an entry for the given atom's \a _id.
  *
@@ -563 +598 @@
   bool FirstTimestep = isPresentadditionalAtomData(newAtom->getId()) ? false : true;
   ASSERT((FirstTimestep && (_step == 0)) || (!FirstTimestep && (_step !=0)),
-      "PdbParser::readAtomDataLine() - logig mismatch between FirstTimestep and step == 0.");
+      "PdbParser::readAtomDataLine() - additionalAtomData present though atom is newly parsed.");
   if (FirstTimestep) {
     LOG(3,"INFO: Parsing new atom.");

src/Parser/PdbParser.hpp

@@ -33 +33 @@
   bool operator==(const PdbParser& b) const;
   void printAtomInfo(const atom *newAtom) const;
+
+protected:
+  void AtomInserted(atomId_t);
+  void AtomRemoved(atomId_t);
 
 private:

src/Parser/TremoloParser.cpp

@@ -163 +163 @@
     saveLine(file, *atomIt);
   }
+}
+
+/** Add default info, when new atom is added to World.
+ *
+ * @param id of atom
+ */
+void TremoloParser::AtomInserted(atomId_t id)
+{
+  std::map<int, TremoloAtomInfoContainer>::iterator iter = additionalAtomData.find(id);
+  ASSERT(iter == additionalAtomData.end(),
+      "TremoloParser::AtomInserted() - additionalAtomData already present for newly added atom "
+      +toString(id)+".");
+  // don't add entry, as this gives a default resSeq of 0 not the molecule id
+  // additionalAtomData.insert( std::make_pair(id, TremoloAtomInfoContainer()) );
+}
+
+/** Remove additional AtomData info, when atom has been removed from World.
+ *
+ * @param id of atom
+ */
+void TremoloParser::AtomRemoved(atomId_t id)
+{
+  std::map<int, TremoloAtomInfoContainer>::iterator iter = additionalAtomData.find(id);
+  // as we do not insert AtomData on AtomInserted, we cannot be assured of its presence
+//  ASSERT(iter != additionalAtomData.end(),
+//      "TremoloParser::AtomRemoved() - additionalAtomData is not present for atom "
+//      +toString(id)+" to remove.");
+  if (iter != additionalAtomData.end())
+    additionalAtomData.erase(iter);
 }
 

src/Parser/TremoloParser.hpp

@@ -38 +38 @@
   void createKnownTypesByIdentity();
   void setAtomData(const std::string &atomdata_string);
+
+protected:
+  void AtomInserted(atomId_t);
+  void AtomRemoved(atomId_t);
 
 private: