Changeset 4b5cf8

Timestamp:

Mar 1, 2011, 10:16:39 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:

b9772a

Parents:

458c31

git-author:

Frederik Heber <heber@…> (02/21/11 13:13:04)

git-committer:

Frederik Heber <heber@…> (03/01/11 10:16:39)

Message:

BondedParticle::OutputBondOfAtom() now takes stream to print to.

Location:

src

Files:

• atom_bondedparticle.cpp (modified) (1 diff)
• atom_bondedparticle.hpp (modified) (1 diff)
• molecule.cpp (modified) (1 diff)
• molecule_graph.cpp (modified) (1 diff)
• unittests/CountBondsUnitTest.cpp (modified) (1 diff)

src/atom_bondedparticle.cpp

@@ -56 +56 @@
 /** Prints all bonds of this atom with total degree.
  */
-void BondedParticle::OutputBondOfAtom() const
-{
-  const BondList& ListOfBonds = getListOfBonds();
-  DoLog(4) && (Log() << Verbose(4) << "Atom " << getName() << "/" << getNr() << " with " << ListOfBonds.size() << " bonds: " << endl);
+void BondedParticle::OutputBondOfAtom(std::ostream &ost) const
+{
+  const BondList& ListOfBonds = getListOfBonds();
+  ost << "Atom " << getName() << "/" << getNr() << " with " << ListOfBonds.size() << " bonds: ";
   int TotalDegree = 0;
   for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); ++Runner) {
-    DoLog(4) && (Log() << Verbose(4) << **Runner << endl);
+    ost << **Runner << "\t";
     TotalDegree += (*Runner)->BondDegree;
   }
-  DoLog(4) && (Log() << Verbose(4) << " -- TotalDegree: " << TotalDegree << endl);
+  ost << " -- TotalDegree: " << TotalDegree;
 };
 

src/atom_bondedparticle.hpp

@@ -45 +45 @@
   int CountBonds() const;
   int CorrectBondDegree();
-  void OutputBondOfAtom() const;
+  void OutputBondOfAtom(std::ostream &ost) const;
   void OutputAdjacency(ofstream * const AdjacencyFile) const;
   void OutputBonds(ofstream * const BondFile) const;

src/molecule.cpp

@@ -942 +942 @@
 void molecule::OutputListOfBonds() const
 {
-  DoLog(2) && (Log() << Verbose(2) << endl << "From Contents of ListOfBonds, all non-hydrogen atoms:" << endl);
-  for_each(atoms.begin(),atoms.end(),mem_fun(&atom::OutputBondOfAtom));
-  DoLog(0) && (Log() << Verbose(0) << endl);
-};
+  std::stringstream output;
+  LOG(2, "From Contents of ListOfBonds, all atoms:");
+  for (molecule::const_iterator iter = begin();
+      iter != end();
+      ++iter) {
+    (*iter)->OutputBondOfAtom(output);
+    output << std::endl << "\t\t";
+  }
+  LOG(2, output.str());
+}
 
 /** Output of element before the actual coordination list.

src/molecule_graph.cpp

@@ -220 +220 @@
 
     // output bonds for debugging (if bond chain list was correctly installed)
-    for_each(atoms.begin(),atoms.end(),mem_fun(&atom::OutputBondOfAtom));
+    for(molecule::internal_iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
+      (*iter)->OutputBondOfAtom((std::ostream &)std::cout);
   } else
     DoLog(1) && (Log() << Verbose(1) << "AtomCount is " << getAtomCount() << ", thus no bonds, no connections!." << endl);

src/unittests/CountBondsUnitTest.cpp

@@ -115 +115 @@
   CPPUNIT_ASSERT_EQUAL( true , BG->CreateAdjacencyForMolecule(TestMolecule2) );
 //  TestMolecule1->Output((ofstream *)&cout);
-//  TestMolecule1->OutputBondsList();
+//  TestMolecule1->OutputBondsList(std::cout);
 };