Changeset 45b45d for src/Parser/PdbParser.cpp

Timestamp:

Feb 9, 2016, 7:11:37 AM (9 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:

d93d2c

Parents:

7daf73

git-author:

Frederik Heber <heber@…> (02/08/16 10:26:55)

git-committer:

Frederik Heber <heber@…> (02/09/16 07:11:37)

Message:

FIX: PdbParser would calculate trajectors over all atoms, not just given set.

• this is only to determine maximum number of trajectory steps but nonetheless unnecessary.

File:

• src/Parser/PdbParser.cpp (modified) (5 diffs)

src/Parser/PdbParser.cpp

@@ -202 +202 @@
   // check for maximum number of time steps
   size_t max_timesteps = 0;
-  BOOST_FOREACH(const atom * _atom, const_cast<const World &>(World::getInstance()).getAllAtoms()) {
-    LOG(4, "INFO: Atom " << _atom->getName() << " " << *dynamic_cast<const AtomInfo *>(_atom) << ".");
+  for (vector<const atom *>::const_iterator atomIt = AtomList.begin();
+      atomIt != AtomList.end(); atomIt++) {
+    const atom * _atom = *atomIt;
+    LOG(4, "INFO: Atom " << _atom->getName() << " "
+        << *dynamic_cast<const AtomInfo *>(_atom) << ".");
     if (_atom->getTrajectorySize() > max_timesteps)
       max_timesteps = _atom->getTrajectorySize();
@@ -213 +216 @@
   // (new atoms might have been added)
   int AtomNo = 1; // serial number starts at 1 in pdb
-  for (vector<const 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());
@@ -240 +244 @@
       std::map<size_t,size_t> MolIdMap;
       size_t MolNo = 1;  // residue number starts at 1 in pdb
-      for (vector<const 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())) {
@@ -256 +261 @@
 
       // write ATOMs
-      for (vector<const 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
@@ -300 +306 @@
 
       // write CONECTs
-      for (vector<const 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);
       }