Changeset 16462f for src/Parser/PdbAtomInfoContainer.cpp

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.cpp (modified) (9 diffs)

src/Parser/PdbAtomInfoContainer.cpp

@@ -24 +24 @@
 #include "Helpers/toString.hpp"
 //#include "Helpers/Verbose.hpp"
+#include "LinearAlgebra/Vector.hpp"
 #include "PdbAtomInfoContainer.hpp"
 
 
 PdbAtomInfoContainer::PdbAtomInfoContainer() :
+  token("ATOM"),
   serial(0),
   name("-"),
-  altloc('0'),
+  altLoc('0'),
   resName("-"),
   chainID('0'),
@@ -37 +39 @@
   occupancy(0.),
   tempFactor(0.),
+  element(""),
   charge(0)
 {}
@@ -46 +49 @@
 {
   switch (key) {
+    case PdbKey::token :
+      ScanKey(token, value);
+      break;
     case PdbKey::serial :
       ScanKey(serial, value);
@@ -52 +58 @@
       ScanKey(name, value);
       break;
-    case PdbKey::altloc :
-      ScanKey(altloc, value);
+    case PdbKey::altLoc :
+      ScanKey(altLoc, value);
       break;
     case PdbKey::resName :
@@ -67 +73 @@
       ScanKey(iCode, value);
       break;
+    case PdbKey::X :
+      ScanKey(XYZ[0], value);
+      break;
+    case PdbKey::Y :
+      ScanKey(XYZ[1], value);
+      break;
+    case PdbKey::Z :
+      ScanKey(XYZ[2], value);
+      break;
     case PdbKey::occupancy :
       ScanKey(occupancy, value);
@@ -72 +87 @@
     case PdbKey::tempFactor :
       ScanKey(tempFactor, value);
+      break;
+    case PdbKey::element :
+      ScanKey(element, value);
       break;
     case PdbKey::charge :
@@ -82 +100 @@
 }
 
-std::string PdbAtomInfoContainer::get(const PdbKey::PdbDataKey key) const
+template <>
+std::string PdbAtomInfoContainer::get<std::string>(const PdbKey::PdbDataKey key) const
 {
   switch (key) {
+    case PdbKey::token :
+      return toString(token);
     case PdbKey::serial :
       return toString(serial);
     case PdbKey::name :
       return toString(name);
-    case PdbKey::altloc :
-      return toString(altloc);
+    case PdbKey::altLoc :
+      return toString(altLoc);
     case PdbKey::resName :
       return toString(resName);
@@ -99 +120 @@
     case PdbKey::iCode :
       return toString(iCode);
+    case PdbKey::X :
+      return toString(XYZ[0]);
+    case PdbKey::Y :
+      return toString(XYZ[1]);
+    case PdbKey::Z :
+      return toString(XYZ[2]);
     case PdbKey::occupancy :
       return toString(occupancy);
     case PdbKey::tempFactor :
       return toString(tempFactor);
+    case PdbKey::element :
+      return toString(element);
     case PdbKey::charge :
       return toString(charge);
@@ -111 +140 @@
 }
 
+template <>
+int PdbAtomInfoContainer::get<int>(const PdbKey::PdbDataKey key) const
+{
+  switch (key) {
+    case PdbKey::serial :
+      return serial;
+    case PdbKey::resSeq :
+      return resSeq;
+    case PdbKey::charge :
+      return charge;
+    default :
+      std::cout << "Unknown key or not presentable as int: " << key << std::endl;
+      return 0;
+  }
+}
+
+template <>
+double PdbAtomInfoContainer::get<double>(const PdbKey::PdbDataKey key) const
+{
+  switch (key) {
+    case PdbKey::X :
+      return XYZ[0];
+    case PdbKey::Y :
+      return XYZ[1];
+    case PdbKey::Z :
+      return XYZ[2];
+    case PdbKey::occupancy :
+      return occupancy;
+    case PdbKey::tempFactor :
+      return tempFactor;
+    default :
+      std::cout << "Unknown key or not presentable as double: " << key << std::endl;
+      return 0.;
+  }
+}