Changeset a479fa for src/molecule.cpp

Timestamp:

Mar 1, 2011, 10:16:38 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:

735b1c

Parents:

5702cdb

git-author:

Frederik Heber <heber@…> (02/21/11 23:50:41)

git-committer:

Frederik Heber <heber@…> (03/01/11 10:16:38)

Message:

Renamed ParticleInfo::nr to ParticleInfo::ParticleInfo_nr for easier privatization.

File:

• src/molecule.cpp (modified) (8 diffs)

src/molecule.cpp

@@ -230 +230 @@
   OBSERVE;
   if (pointer != NULL) {
-    pointer->sort = &pointer->nr;
+    pointer->sort = &pointer->ParticleInfo_nr;
     if (pointer->getType() != NULL) {
       if (pointer->getType()->getAtomicNumber() != 1)
@@ -236 +236 @@
       if(pointer->getName() == "Unknown"){
         stringstream sstr;
-        sstr << pointer->getType()->getSymbol() << pointer->nr+1;
+        sstr << pointer->getType()->getSymbol() << pointer->ParticleInfo_nr+1;
         pointer->setName(sstr.str());
       }
@@ -258 +258 @@
     atom *walker = pointer->clone();
     walker->setName(pointer->getName());
-    walker->nr = last_atom++;  // increase number within molecule
+    walker->setNr(last_atom++);  // increase number within molecule
     insert(walker);
     if ((pointer->getType() != NULL) && (pointer->getType()->getAtomicNumber() != 1))
@@ -723 +723 @@
   ASSERT(atom1, "First atom in bond-creation was an invalid pointer");
   ASSERT(atom2, "Second atom in bond-creation was an invalid pointer");
-  ASSERT(FindAtom(atom1->nr),"First atom in bond-creation was not part of molecule");
-  ASSERT(FindAtom(atom2->nr),"Second atom in bond-creation was not part of molecule");
+  ASSERT(FindAtom(atom1->ParticleInfo_nr),"First atom in bond-creation was not part of molecule");
+  ASSERT(FindAtom(atom2->ParticleInfo_nr),"Second atom in bond-creation was not part of molecule");
 
   Binder = new bond(atom1, atom2, degree, BondCount++);
@@ -839 +839 @@
   molecule::const_iterator iter = begin();
   for (; iter != end(); ++iter)
-    if ((*iter)->nr == Nr)
+    if ((*iter)->ParticleInfo_nr == Nr)
       break;
   if (iter != end()) {
-    //Log() << Verbose(0) << "Found Atom Nr. " << walker->nr << endl;
+    //Log() << Verbose(0) << "Found Atom Nr. " << walker->ParticleInfo_nr << endl;
     return (*iter);
   } else {
@@ -984 +984 @@
   NoNonHydrogen = 0;
   for (molecule::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
-    (*iter)->nr = i;   // update number in molecule (for easier referencing in FragmentMolecule lateron)
+    (*iter)->setNr(i);   // update number in molecule (for easier referencing in FragmentMolecule lateron)
     if ((*iter)->getType()->getAtomicNumber() != 1) // count non-hydrogen atoms whilst at it
       NoNonHydrogen++;
     stringstream sstr;
-    sstr << (*iter)->getType()->getSymbol() << (*iter)->nr+1;
+    sstr << (*iter)->getType()->getSymbol() << (*iter)->ParticleInfo_nr+1;
     (*iter)->setName(sstr.str());
-    DoLog(3) && (Log() << Verbose(3) << "Naming atom nr. " << (*iter)->nr << " " << (*iter)->getName() << "." << endl);
+    DoLog(3) && (Log() << Verbose(3) << "Naming atom nr. " << (*iter)->ParticleInfo_nr << " " << (*iter)->getName() << "." << endl);
     i++;
   }
@@ -1017 +1017 @@
     for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
       if ((*iter)->father == NULL) {
-        AtomicMap[(*iter)->nr] = -2;
+        AtomicMap[(*iter)->ParticleInfo_nr] = -2;
       } else {
         for (molecule::const_iterator runner = OtherMolecule->begin(); runner != OtherMolecule->end(); ++runner) {
@@ -1024 +1024 @@
           //Log() << Verbose(4) << "Comparing father " << (*iter)->father << " with the other one " << (*runner)->father << "." << endl;
           if ((*iter)->father == (*runner))
-            AtomicMap[(*iter)->nr] = (*runner)->nr;
+            AtomicMap[(*iter)->ParticleInfo_nr] = (*runner)->ParticleInfo_nr;
         }
       }
-      DoLog(0) && (Log() << Verbose(0) << AtomicMap[(*iter)->nr] << "\t");
+      DoLog(0) && (Log() << Verbose(0) << AtomicMap[(*iter)->ParticleInfo_nr] << "\t");
     }
     DoLog(0) && (Log() << Verbose(0) << endl);