Changeset b0a2e3 for src/Parser

Timestamp:

Feb 24, 2011, 8:18:39 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:

3e383d

Parents:

09c7a9

Message:

Removed use of PdbKey::timestep, steps are parsed sequentially.

• PdbParser::readAtomDataLine() and PdbParser::readNeighbors() have additional parameter steps.

Location:

src/Parser

Files:

• PdbParser.cpp (modified) (6 diffs)
• PdbParser.hpp (modified) (1 diff)

src/Parser/PdbParser.cpp

@@ -116 +116 @@
   molecule *newmol = World::getInstance().createMolecule();
   newmol->ActiveFlag = true;
+  unsigned int step = 0;
   // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
   World::getInstance().getMolecules()->insert(newmol);
   while (NotEndOfFile) {
     bool NotEndOfTimestep = true;
-    while (NotEndOfTimestep) {
+    while (NotEndOfTimestep && NotEndOfFile) {
       std::getline(*file, line, '\n');
-      // extract first token
-      token = getToken(line);
-      switch (token) {
-        case PdbKey::Atom:
-          LOG(3,"INFO: Parsing ATOM entry.");
-          readAtomDataLine(line, newmol);
-          break;
-        case PdbKey::Remark:
-          LOG(3,"INFO: Parsing REM entry.");
-          break;
-        case PdbKey::Connect:
-          LOG(3,"INFO: Parsing CONECT entry.");
-          readNeighbors(line);
-          break;
-        case PdbKey::Filler:
-          LOG(3,"INFO: Stumbled upon Filler entry.");
-          break;
-        case PdbKey::EndOfTimestep:
-          LOG(3,"INFO: Parsing END entry or empty line.");
-          NotEndOfTimestep = false;
-          break;
-        default:
-          // TODO: put a throw here
-          DoeLog(2) && (eLog() << Verbose(2) << "Unknown token: '" << line << "'" << std::endl);
-          //ASSERT(0, "PdbParser::load() - Unknown token in line "+toString(linecount)+": "+line+".");
-          break;
+      if (!line.empty()) {
+        // extract first token
+        token = getToken(line);
+        switch (token) {
+          case PdbKey::Atom:
+            LOG(3,"INFO: Parsing ATOM entry for time step " << step << ".");
+            readAtomDataLine(step, line, newmol);
+            break;
+          case PdbKey::Remark:
+            LOG(3,"INFO: Parsing REM entry for time step " << step << ".");
+            break;
+          case PdbKey::Connect:
+            LOG(3,"INFO: Parsing CONECT entry for time step " << step << ".");
+            readNeighbors(step, line);
+            break;
+          case PdbKey::Filler:
+            LOG(3,"INFO: Stumbled upon Filler entry for time step " << step << ".");
+            break;
+          case PdbKey::EndOfTimestep:
+            LOG(3,"INFO: Parsing END entry or empty line for time step " << step << ".");
+            NotEndOfTimestep = false;
+            break;
+          default:
+            // TODO: put a throw here
+            DoeLog(2) && (eLog() << Verbose(2) << "Unknown token: '" << line << "' for time step " << step << "." << std::endl);
+            //ASSERT(0, "PdbParser::load() - Unknown token in line "+toString(linecount)+": "+line+".");
+            break;
+        }
       }
       NotEndOfFile = NotEndOfFile && (file->good());
       linecount++;
+    }
+    ++step;
+  }
+  BOOST_FOREACH(atom *_atom, World::getInstance().getAllAtoms()) {
+    for (size_t i=0; i < _atom->getTrajectorySize(); ++i) {
+      LOG(2, "INFO: Atom " << _atom->getName() << " is at "
+          << _atom->getPositionAtStep(i) << " at time step " << i << ".");
     }
   }
@@ -491 +501 @@
  *  standard information is placed in additionalAtomData at the atom's id.
  *
+ * \param _step time step to use
  * \param line to parse as an atom
  * \param newmol molecule to add parsed atoms to
  */
-void PdbParser::readAtomDataLine(std::string &line, molecule *newmol = NULL) {
+void PdbParser::readAtomDataLine(const unsigned int _step, std::string &line, molecule *newmol = NULL) {
   vector<string>::iterator it;
 
@@ -500 +511 @@
   LOG(3,"INFO: Parsing END entry or empty line.");
   bool FirstTimestep = isPresentadditionalAtomData(newAtom->getId()) ? false : true;
+  ASSERT((FirstTimestep && (_step == 0)) || (!FirstTimestep && (_step !=0)),
+      "PdbParser::readAtomDataLine() - logig mismatch between FirstTimestep and step == 0.");
   if (FirstTimestep) {
     LOG(3,"INFO: Parsing new atom.");
@@ -619 +632 @@
     PdbAtomInfoContainer::ScanKey(tempVector[1], line.substr(38,8));
     PdbAtomInfoContainer::ScanKey(tempVector[2], line.substr(46,8));
-    // increase time step
-    size_t timestep = atomInfo.get<size_t>(PdbKey::timestep)+1;
-    atomInfo.set(PdbKey::timestep, toString(timestep));
-    LOG(4,"INFO: Adding time step "+atomInfo.get<std::string>(PdbKey::timestep)+".");
+    LOG(4,"INFO: Adding trajectory point to time step "+toString(_step)+".");
     // and set position at new time step
-    newAtom->setPositionAtStep(timestep, tempVector);
+    newAtom->setPositionAtStep(_step, tempVector);
   }
 
@@ -659 +669 @@
  * Reads neighbor information for one atom from the input.
  *
+ * \param _step time step to use
  * \param line to parse as an atom
  */
-void PdbParser::readNeighbors(std::string &line)
+void PdbParser::readNeighbors(const unsigned int _step, std::string &line)
 {
   const size_t length = line.length();
@@ -693 +704 @@
 //    DoLog(1) && (Log() << Verbose(1) << "Adding Bond (" << getAtomId(id) << "," << getAtomId(*iter) << ")" << std::endl);
     atom * const _Otheratom = World::getInstance().getAtom(AtomById(getSerial(*iter)));
-    _atom->addBond(WorldTime::getTime(), _Otheratom);
+    _atom->addBond(_step, _Otheratom);
   }
 }

src/Parser/PdbParser.hpp

@@ -36 +36 @@
 private:
   enum PdbKey::KnownTokens getToken(string &line);
-  void readAtomDataLine(string &line, molecule *newmol);
+  void readAtomDataLine(const unsigned int _step, string &line, molecule *newmol);
   void parseAtomDataKeysLine(string line, int offset);
-  void readNeighbors(std::string &line);
+  void readNeighbors(const unsigned int _step, std::string &line);
 //  void adaptImprData();
 //  void adaptTorsion();