Changeset 93fd43e for src/Parser

Timestamp:

Dec 16, 2010, 5:32:22 PM (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:

0bbfa1

Parents:

1d02fe3

git-author:

Frederik Heber <heber@…> (12/07/10 14:00:19)

git-committer:

Frederik Heber <heber@…> (12/16/10 17:32:22)

Message:

new function PdbParser::getadditionalAtomData() that also adds new entries.

• either we get the present one, or create from next father, topmost father or from defaultValues a new entry.

Location:

src/Parser

Files:

• PdbParser.cpp (modified) (4 diffs)
• PdbParser.hpp (modified) (1 diff)

src/Parser/PdbParser.cpp

@@ -151 +151 @@
 void PdbParser::save(ostream* file) {
   DoLog(0) && (Log() << Verbose(0) << "Saving changes to pdb." << std::endl);
-
   {
     // add initial remark
@@ -190 +189 @@
     int AtomNo = 1; // serial number starts at 1 in pdb
     for (vector<atom *>::iterator atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
-      PdbAtomInfoContainer &atomInfo = additionalAtomData[(*atomIt)->getId()];
+      PdbAtomInfoContainer &atomInfo = getadditionalAtomData(*atomIt);
       // gather info about residue
       const molecule *mol = (*atomIt)->getMolecule();
@@ -241 +240 @@
 }
 
+/** Either returns reference to present entry or creates new with default values.
+ *
+ * @param _atom atom whose entry we desire
+ * @return
+ */
+PdbAtomInfoContainer& PdbParser::getadditionalAtomData(atom *_atom)
+{
+  if (additionalAtomData.find(_atom->getId()) != additionalAtomData.end()) {
+  } else if (additionalAtomData.find(_atom->father->getId()) != additionalAtomData.end()) {
+    // use info from direct father
+    additionalAtomData[_atom->getId()] = additionalAtomData[_atom->father->getId()];
+  } else if (additionalAtomData.find(_atom->GetTrueFather()->getId()) != additionalAtomData.end()) {
+    // use info from topmost father
+    additionalAtomData[_atom->getId()] = additionalAtomData[_atom->GetTrueFather()->getId()];
+  } else {
+    // create new entry use default values if nothing else is known
+    additionalAtomData[_atom->getId()] = defaultAdditionalData;
+  }
+  return additionalAtomData[_atom->getId()];
+}
+
 /**
  * Writes one line of PDB-formatted data to the provided stream.
@@ -366 +386 @@
   stringstream lineStream;
   atom* newAtom = World::getInstance().createAtom();
-  additionalAtomData[newAtom->getId()] = PdbAtomInfoContainer();
-  PdbAtomInfoContainer &atomInfo = additionalAtomData[newAtom->getId()];
+  PdbAtomInfoContainer &atomInfo = getadditionalAtomData(newAtom);
   string word;
   ConvertTo<size_t> toSize_t;

src/Parser/PdbParser.hpp

@@ -41 +41 @@
 
   // internal getter and setter
+  PdbAtomInfoContainer& getadditionalAtomData(atom *_atom);
   size_t getSerial(const size_t atomid) const;
   void setSerial(const size_t localatomid, const size_t atomid);