Changeset fac58f for src/Parser/PdbParser.hpp

Timestamp:

Jul 24, 2015, 4:44:35 PM (10 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:

f3b597

Parents:

99db9b

git-author:

Frederik Heber <heber@…> (06/02/15 08:52:11)

git-committer:

Frederik Heber <heber@…> (07/24/15 16:44:35)

Message:

Converted FormatParser::save() to using vector of const atom ptrs.

• required to change all save() functions in all parsers.

File:

• src/Parser/PdbParser.hpp (modified) (2 diffs)

src/Parser/PdbParser.hpp

@@ -53 +53 @@
   virtual ~FormatParser();
   void load(std::istream* file);
-  void save(std::ostream* file, const std::vector<atom *> &atoms);
+  void save(std::ostream* file, const std::vector<const atom *> &atoms);
 
   bool operator==(const FormatParser< pdb>& b) const;
-  void printAtomInfo(const atom *newAtom) const;
+  void printAtomInfo(const atom * const newAtom) const;
 
 protected:
@@ -71 +71 @@
 //  std::string adaptIdDependentDataString(std::string data);
   bool isUsedField(std::string fieldName);
-  void writeNeighbors(std::ostream* file, int numberOfNeighbors, atom* currentAtom);
+  void writeNeighbors(std::ostream* file, int numberOfNeighbors, const atom* currentAtom);
   void saveLine(std::ostream* file, const PdbAtomInfoContainer &atomInfo);
 
   // internal getter and setter
   bool isPresentadditionalAtomData(const atomId_t _id) const;
-  PdbAtomInfoContainer& getadditionalAtomData(atom *_atom);
+  PdbAtomInfoContainer& getadditionalAtomData(const atom *_atom);
 
   // internal helper functions