Changeset 16462f for src/Parser/PdbAtomInfoContainer.hpp

Timestamp:

Dec 16, 2010, 5:32:18 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:

1d02fe3

Parents:

24f128

git-author:

Frederik Heber <heber@…> (12/07/10 12:54:42)

git-committer:

Frederik Heber <heber@…> (12/16/10 17:32:18)

Message:

PdbParser is now complete with respect to additionalAtomData.

• serial, name, resName, resSeq, element, and charge are updated if changed, otherwise we use values from PdbAtomInfoContainer.
• PdbParser::saveLine() completely uses information from PdbAtomInfoContainer.

Testchanges:

• Simple_configuration/2/post/test.pdb updated as we are now closer to real PDB format also concerning alignment and the resName changed again.

File:

• src/Parser/PdbAtomInfoContainer.hpp (modified) (3 diffs)

src/Parser/PdbAtomInfoContainer.hpp

@@ -11 +11 @@
 #include "PdbKey.hpp"
 
+class Vector;
+
 #include <string>
+#include <typeinfo>
 
 /**
@@ -22 +25 @@
 
   // getter and setter
-  std::string get(const PdbKey::PdbDataKey key) const;
+  template <class T> T get(const PdbKey::PdbDataKey key) const  {
+    switch (key) {
+      default :
+        std::cout << "Unknown key or not representable as " << typeid(T).name() << ": " << key << std::endl;
+        break;
+    }
+    return (T)NULL;
+  }
   void set(const PdbKey::PdbDataKey key, std::string value);
 
@@ -46 +56 @@
 
 private:
+  std::string token;
   int serial;
   std::string name;
-  char altloc;
+  char altLoc;
   std::string resName;
   char chainID;
   int resSeq;
   char iCode;
+  Vector XYZ;
   float occupancy;
   float tempFactor;
+  std::string element;
   int charge;
 };
 
+template <>
+std::string PdbAtomInfoContainer::get<std::string>(const PdbKey::PdbDataKey key) const;
+template <>
+int PdbAtomInfoContainer::get<int>(const PdbKey::PdbDataKey key) const;
+template <>
+double PdbAtomInfoContainer::get<double>(const PdbKey::PdbDataKey key) const;
+
 #endif /* PDBATOMINFOCONTAINER_HPP_ */