Changeset 9dba5f for src/Parser/PdbAtomInfoContainer.cpp

Timestamp:

Feb 24, 2011, 7:55:15 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:

873037

Parents:

fcac72

git-author:

Frederik Heber <heber@…> (02/10/11 22:01:26)

git-committer:

Frederik Heber <heber@…> (02/24/11 19:55:15)

Message:

PdbParser can now load and save multiple time steps.

• WARNING: Molecules are not yet updated, it only works on simple test.
• TEST: Parser/Pdb regression test on loading/storing multiple steps added.
• PdbAtomInfoContainer:
  • private static knownDataKeys map from enum to strings, filled in cstor when empty by fillknownDataKeys() and cleared by befriended PdbParser's dstor.
  • operator << to easily print container.
  • getter function getDataKey.
• PdbKey:
  • EndOfFile -> EndOfTimestep.
  • new DataKey timestep to allow storing of timestep.
• Pdbparser:
  • extended load() and added verbosity.
  • readAtomDataLine() can parse trajectories into present atoms.
  • extended save() and added verbosity.
  • new helper functions getAtomToParse() and readPdbAtomInfoContainer().

File:

• src/Parser/PdbAtomInfoContainer.cpp (modified) (7 diffs)

src/Parser/PdbAtomInfoContainer.cpp

@@ -20 +20 @@
 #include "CodePatterns/MemDebug.hpp"
 
-//#include "CodePatterns/Assert.hpp"
+#include "CodePatterns/Assert.hpp"
 //#include "CodePatterns/Log.hpp"
 #include "CodePatterns/toString.hpp"
@@ -27 +27 @@
 #include "PdbAtomInfoContainer.hpp"
 
+PdbAtomInfoContainer::knownDataKeysMap PdbAtomInfoContainer::knownDataKeys;
 
 PdbAtomInfoContainer::PdbAtomInfoContainer() :
@@ -40 +41 @@
   tempFactor(0.),
   element(""),
-  charge(0)
-{}
+  charge(0),
+  timestep(0)
+{
+  if (knownDataKeys.empty())
+    fillknownDataKeys();
+}
 
 PdbAtomInfoContainer::~PdbAtomInfoContainer()
 {}
 
+void PdbAtomInfoContainer::fillknownDataKeys()
+{
+  knownDataKeys[PdbKey::token] = "token";
+  knownDataKeys[PdbKey::serial] = "serial";
+  knownDataKeys[PdbKey::name] = "name";
+  knownDataKeys[PdbKey::altLoc] = "altLoc";
+  knownDataKeys[PdbKey::resName] = "resName";
+  knownDataKeys[PdbKey::chainID] = "chainID";
+  knownDataKeys[PdbKey::resSeq] = "resSeq";
+  knownDataKeys[PdbKey::iCode] = "iCode";
+  knownDataKeys[PdbKey::X] = "X";
+  knownDataKeys[PdbKey::Y] = "Y";
+  knownDataKeys[PdbKey::Z] = "Z";
+  knownDataKeys[PdbKey::occupancy] = "occupancy";
+  knownDataKeys[PdbKey::tempFactor] = "tempFactor";
+  knownDataKeys[PdbKey::element] = "element";
+  knownDataKeys[PdbKey::charge] = "charge";
+  knownDataKeys[PdbKey::timestep] = "timestep";
+}
+
 void PdbAtomInfoContainer::set(const PdbKey::PdbDataKey key, std::string value)
 {
@@ -93 +118 @@
     case PdbKey::charge :
       ScanKey(charge, value);
+      break;
+    case PdbKey::timestep :
+      ScanKey(timestep, value);
       break;
     default :
@@ -134 +162 @@
     case PdbKey::charge :
       return toString(charge);
+    case PdbKey::timestep :
+      return toString(timestep);
     default :
       std::cout << "Unknown key: " << key << std::endl;
@@ -150 +180 @@
     case PdbKey::charge :
       return charge;
+    case PdbKey::timestep :
+      return timestep;
     default :
       std::cout << "Unknown key or not presentable as int: " << key << std::endl;
@@ -175 +207 @@
   }
 }
+
+const std::string& PdbAtomInfoContainer::getDataKey(PdbKey::PdbDataKey key) const
+{
+  knownDataKeysMap::const_iterator iter;
+  iter = knownDataKeys.find(key);
+  ASSERT(iter != knownDataKeys.end(),
+      "PdbAtomInfoContainer::getDataKey() - unknown key "
+      +toString(key)+" request, did someone add a key to PdbKey?");
+  return iter->second;
+}
+
+std::ostream& operator<<(std::ostream &ost, const PdbAtomInfoContainer& m)
+{
+  ost << m.getDataKey(PdbKey::token) << "(" << m.get<std::string>(PdbKey::token) <<") ";
+  ost << m.getDataKey(PdbKey::serial) << "(" << m.get<std::string>(PdbKey::serial) <<") ";
+  ost << m.getDataKey(PdbKey::name) << "(" << m.get<std::string>(PdbKey::name) <<") ";
+  ost << m.getDataKey(PdbKey::altLoc) << "(" << m.get<std::string>(PdbKey::altLoc) <<") ";
+  ost << m.getDataKey(PdbKey::resName) << "(" << m.get<std::string>(PdbKey::resName) <<") ";
+  ost << m.getDataKey(PdbKey::chainID) << "(" << m.get<std::string>(PdbKey::chainID) <<") ";
+  ost << m.getDataKey(PdbKey::resSeq) << "(" << m.get<std::string>(PdbKey::resSeq) <<") ";
+  ost << m.getDataKey(PdbKey::iCode) << "(" << m.get<std::string>(PdbKey::iCode) <<") ";
+  ost << m.getDataKey(PdbKey::X) << "(" << m.get<std::string>(PdbKey::X) <<") ";
+  ost << m.getDataKey(PdbKey::Y) << "(" << m.get<std::string>(PdbKey::Y) <<") ";
+  ost << m.getDataKey(PdbKey::Z) << "(" << m.get<std::string>(PdbKey::Z) <<") ";
+  ost << m.getDataKey(PdbKey::occupancy) << "(" << m.get<std::string>(PdbKey::occupancy) <<") ";
+  ost << m.getDataKey(PdbKey::tempFactor) << "(" << m.get<std::string>(PdbKey::tempFactor) <<") ";
+  ost << m.getDataKey(PdbKey::element) << "(" << m.get<std::string>(PdbKey::element) <<") ";
+  ost << m.getDataKey(PdbKey::charge) << "(" << m.get<std::string>(PdbKey::charge) <<") ";
+  ost << m.getDataKey(PdbKey::timestep) << "(" << m.get<std::string>(PdbKey::timestep) <<") ";
+  return ost;
+}