Changeset 9d83b6 for src/Parser

Timestamp:

Feb 24, 2011, 6:51:32 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:

a2bdbe

Parents:

c0d9eb

git-author:

Frederik Heber <heber@…> (02/24/11 14:41:13)

git-committer:

Frederik Heber <heber@…> (02/24/11 18:51:32)

Message:

BondedParticleInfo now has vector<BondList>

• vector<BondList> ListOfBonds is private, getter for (non-)const access.
• Access everywhere to ListOfBonds replaced by respective getter.
• Access is as of now always to time step zero.
• greatest impact is on molecule... files, and ListOfBondsUnitTest.

Location:

src/Parser

Files:

• PdbParser.cpp (modified) (2 diffs)
• TremoloParser.cpp (modified) (3 diffs)

src/Parser/PdbParser.cpp

@@ -325 +325 @@
  * Writes the neighbor information of one atom to the provided stream.
  *
+ * Note that ListOfBonds of WorldTime::CurrentTime is used.
+ *
  * \param *file  where to write neighbor information to
  * \param MaxnumberOfNeighbors of neighbors
@@ -331 +333 @@
 void PdbParser::writeNeighbors(ostream* file, int MaxnumberOfNeighbors, atom* currentAtom) {
   int MaxNo = MaxnumberOfNeighbors;
-  if (!currentAtom->ListOfBonds.empty()) {
-    for(BondList::iterator currentBond = currentAtom->ListOfBonds.begin(); currentBond != currentAtom->ListOfBonds.end(); ++currentBond) {
+  const BondList & ListOfBonds = currentAtom->getListOfBonds();
+  if (!ListOfBonds.empty()) {
+    for(BondList::const_iterator currentBond = ListOfBonds.begin(); currentBond != ListOfBonds.end(); ++currentBond) {
       if (MaxNo >= MaxnumberOfNeighbors) {
         *file << "CONECT";

src/Parser/TremoloParser.cpp

@@ -26 +26 @@
 #include "TremoloParser.hpp"
 #include "World.hpp"
+#include "WorldTime.hpp"
 #include "atom.hpp"
 #include "bond.hpp"
@@ -258 +259 @@
  * Writes the neighbor information of one atom to the provided stream.
  *
+ * Note that ListOfBonds of WorldTime::CurrentTime is used.
+ *
  * \param stream where to write neighbor information to
  * \param number of neighbors
@@ -263 +266 @@
  */
 void TremoloParser::writeNeighbors(ostream* file, int numberOfNeighbors, atom* currentAtom) {
-  BondList::iterator currentBond = currentAtom->ListOfBonds.begin();
+  const BondList& ListOfBonds = currentAtom->getListOfBonds();
+  BondList::const_iterator currentBond = ListOfBonds.begin();
   for (int i = 0; i < numberOfNeighbors; i++) {
-    *file << (currentBond != currentAtom->ListOfBonds.end()
+    *file << (currentBond != ListOfBonds.end()
         ? (*currentBond)->GetOtherAtom(currentAtom)->getId()+1 : 0) << "\t";
-    if (currentBond != currentAtom->ListOfBonds.end())
+    if (currentBond != ListOfBonds.end())
       ++currentBond;
   }