Changeset fac58f for src/Parser/PdbParser.cpp

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, Candidate_v1.7.0, 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.cpp (modified) (7 diffs)

src/Parser/PdbParser.cpp

@@ -194 +194 @@
  * \param atoms atoms to store
  */
-void FormatParser< pdb >::save(ostream* file, const std::vector<atom *> &AtomList)
+void FormatParser< pdb >::save(
+    ostream* file,
+    const std::vector<const atom *> &AtomList)
 {
   LOG(2, "DEBUG: Saving changes to pdb.");
@@ -211 +213 @@
   // (new atoms might have been added)
   int AtomNo = 1; // serial number starts at 1 in pdb
-  for (vector<atom *>::const_iterator atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
+  for (vector<const atom *>::const_iterator atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
     PdbAtomInfoContainer &atomInfo = getadditionalAtomData(*atomIt);
     associateLocaltoGlobalId(AtomNo, (*atomIt)->getId());
@@ -238 +240 @@
       std::map<size_t,size_t> MolIdMap;
       size_t MolNo = 1;  // residue number starts at 1 in pdb
-      for (vector<atom *>::const_iterator atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
+      for (vector<const atom *>::const_iterator atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
         const molecule *mol = (*atomIt)->getMolecule();
         if ((mol != NULL) && (MolIdMap.find(mol->getId()) == MolIdMap.end())) {
@@ -254 +256 @@
 
       // write ATOMs
-      for (vector<atom *>::const_iterator atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
+      for (vector<const atom *>::const_iterator atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
         PdbAtomInfoContainer &atomInfo = getadditionalAtomData(*atomIt);
         // gather info about residue
@@ -298 +300 @@
 
       // write CONECTs
-      for (vector<atom *>::const_iterator atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
+      for (vector<const atom *>::const_iterator atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
         writeNeighbors(file, 4, *atomIt);
       }
@@ -357 +359 @@
  * @return
  */
-PdbAtomInfoContainer& FormatParser< pdb >::getadditionalAtomData(atom *_atom)
+PdbAtomInfoContainer& FormatParser< pdb >::getadditionalAtomData(const atom * const _atom)
 {
   if (additionalAtomData.find(_atom->getId()) != additionalAtomData.end()) {
@@ -498 +500 @@
  * \param *currentAtom to the atom of which to take the neighbor information
  */
-void FormatParser< pdb >::writeNeighbors(ostream* file, int MaxnumberOfNeighbors, atom* currentAtom) {
+void FormatParser< pdb >::writeNeighbors(
+    ostream* file,
+    int MaxnumberOfNeighbors,
+    const atom * const currentAtom) {
   int MaxNo = MaxnumberOfNeighbors;
   int charsleft = 80;