Changeset 8bf9c6

Timestamp:

Feb 17, 2012, 3:24:17 PM (13 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:

812155

Parents:

2ad1ec

git-author:

Frederik Heber <heber@…> (01/06/12 13:11:42)

git-committer:

Frederik Heber <heber@…> (02/17/12 15:24:17)

Message:

All additionalAtomData maps now have const atomId_t as key.

Location:

src/Parser

Files:

• PdbParser.cpp (modified) (3 diffs)
• PdbParser.hpp (modified) (3 diffs)
• TremoloParser.cpp (modified) (15 diffs)
• TremoloParser.hpp (modified) (1 diff)

src/Parser/PdbParser.cpp

@@ -312 +312 @@
 {
   //LOG(3, "FormatParser< pdb >::AtomRemoved() - notified of atom " << id << "'s removal.");
-  std::map<size_t, PdbAtomInfoContainer>::iterator iter = additionalAtomData.find(id);
+  std::map<const atomId_t, PdbAtomInfoContainer>::iterator iter = additionalAtomData.find(id);
   // as we do not insert AtomData on AtomInserted, we cannot be assured of its presence
 //  ASSERT(iter != additionalAtomData.end(),
@@ -328 +328 @@
  * @return true - entry present, false - only for atom's father or no entry
  */
-bool FormatParser< pdb >::isPresentadditionalAtomData(unsigned int _id)
-{
-  return (additionalAtomData.find(_id) != additionalAtomData.end());
+bool FormatParser< pdb >::isPresentadditionalAtomData(const atomId_t _id) const
+{
+  std::map<const atomId_t, PdbAtomInfoContainer>::const_iterator iter = additionalAtomData.find(_id);
+  return (iter != additionalAtomData.end());
 }
 
@@ -480 +481 @@
   if (newAtom == NULL) {
     newAtom = World::getInstance().createAtom();
-    const unsigned int AtomID_global = newAtom->getId();
+    //const unsigned int AtomID_global = newAtom->getId();
     LOG(4, "INFO: No association to global id present, creating atom.");
   } else {

src/Parser/PdbParser.hpp

@@ -21 +21 @@
 #include "FormatParser_common.hpp"
 #include "ParserTypes.hpp"
+#include "types.hpp"
 
 #include "PdbAtomInfoContainer.hpp"
@@ -71 +72 @@
 
   // internal getter and setter
-  bool isPresentadditionalAtomData(unsigned int _id);
+  bool isPresentadditionalAtomData(const atomId_t _id) const;
   PdbAtomInfoContainer& getadditionalAtomData(atom *_atom);
 
@@ -92 +93 @@
    * file.
    */
-  std::map<size_t, PdbAtomInfoContainer> additionalAtomData;
+  std::map<const atomId_t, PdbAtomInfoContainer> additionalAtomData;
 
   /**

src/Parser/TremoloParser.cpp

@@ -37 +37 @@
 #include "WorldTime.hpp"
 
-#include <map>
-#include <vector>
 
 #include <boost/tokenizer.hpp>
 #include <iostream>
 #include <iomanip>
-
-using namespace std;
+#include <map>
+#include <sstream>
+#include <vector>
 
 // declare specialized static variables
@@ -112 +111 @@
  */
 void FormatParser< tremolo >::load(istream* file) {
-  string line;
-  string::size_type location;
+  std::string line;
+  std::string::size_type location;
 
   // reset the id maps
@@ -156 +155 @@
   LOG(0, "Saving changes to tremolo.");
 
-  vector<atom*>::const_iterator atomIt;
+  std::vector<atom*>::const_iterator atomIt;
   /*vector<string>::iterator it;*/
-  vector<string>::iterator it = unique(usedFields.begin(), usedFields.end()); // skips all duplicates in the vector
-
-
-  LOG(3, "usedFields before save contains: " << usedFields);
-
-  LOG(3, "additionalAtomData contains: " << additionalAtomData);
-
-  LOG(3, "additionalAtomData contains: " << additionalAtomData);
+  std::vector<std::string>::iterator it = unique(usedFields.begin(), usedFields.end()); // skips all duplicates in the vector
+
+  LOG(3, "INFO: usedFields before save contains: " << usedFields);
+  //LOG(3, "INFO: additionalAtomData contains: " << additionalAtomData);
 
   *file << "# ATOMDATA";
@@ -183 +178 @@
 void FormatParser< tremolo >::AtomInserted(atomId_t id)
 {
-  std::map<int, TremoloAtomInfoContainer>::iterator iter = additionalAtomData.find(id);
+  std::map<const atomId_t, TremoloAtomInfoContainer>::iterator iter = additionalAtomData.find(id);
   ASSERT(iter == additionalAtomData.end(),
       "FormatParser< tremolo >::AtomInserted() - additionalAtomData already present for newly added atom "
@@ -197 +192 @@
 void FormatParser< tremolo >::AtomRemoved(atomId_t id)
 {
-  std::map<int, TremoloAtomInfoContainer>::iterator iter = additionalAtomData.find(id);
+  std::map<const atomId_t, TremoloAtomInfoContainer>::iterator iter = additionalAtomData.find(id);
   // as we do not insert AtomData on AtomInserted, we cannot be assured of its presence
 //  ASSERT(iter != additionalAtomData.end(),
@@ -225 +220 @@
  */
 void FormatParser< tremolo >::saveLine(ostream* file, atom* currentAtom) {
-  vector<string>::iterator it;
+  std::vector<string>::iterator it;
 
   TremoloKey::atomDataKey currentField;
@@ -343 +338 @@
  */
 void FormatParser< tremolo >::parseAtomDataKeysLine(string line, int offset) {
-  string keyword;
-  stringstream lineStream;
+  std::string keyword;
+  std::stringstream lineStream;
 
   lineStream << line.substr(offset);
@@ -382 +377 @@
  * \param *newmol molecule to add atom to
  */
-void FormatParser< tremolo >::readAtomDataLine(string line, molecule *newmol = NULL) {
-  vector<string>::iterator it;
-  stringstream lineStream;
+void FormatParser< tremolo >::readAtomDataLine(std::string line, molecule *newmol = NULL) {
+  std::vector<string>::iterator it;
+  std::stringstream lineStream;
   atom* newAtom = World::getInstance().createAtom();
   const atomId_t atomid = newAtom->getId();
@@ -406 +401 @@
     const std::string keyName = it->substr(0, it->find("="));
     currentField = knownKeys[keyName];
-    const string word = *tok_iter;
+    const std::string word = *tok_iter;
     LOG(4, "INFO: Parsing key " << keyName << " with remaining data " << word);
     switch (currentField) {
@@ -499 +494 @@
 bool FormatParser< tremolo >::isUsedField(string fieldName) {
   bool fieldNameExists = false;
-  for (vector<string>::iterator usedField = usedFields.begin(); usedField != usedFields.end(); usedField++) {
+  for (std::vector<std::string>::iterator usedField = usedFields.begin(); usedField != usedFields.end(); usedField++) {
     if (usedField->substr(0, usedField->find("=")) == fieldName)
       fieldNameExists = true;
@@ -518 +513 @@
   }
 
-  for(map<int, TremoloAtomInfoContainer>::iterator currentInfo = additionalAtomData.begin();
+  for(std::map<const atomId_t, TremoloAtomInfoContainer>::iterator currentInfo = additionalAtomData.begin();
     currentInfo != additionalAtomData.end(); currentInfo++
   ) {
     if (!currentInfo->second.neighbors_processed) {
-      for(vector<int>::iterator neighbor = currentInfo->second.neighbors.begin();
+      for(std::vector<int>::iterator neighbor = currentInfo->second.neighbors.begin();
         neighbor != currentInfo->second.neighbors.end(); neighbor++
       ) {
@@ -557 +552 @@
   char separator;
   int id;
-  stringstream line, result;
+  std::stringstream line, result;
   line << data;
 
@@ -579 +574 @@
   }
 
-  for(map<int, TremoloAtomInfoContainer>::iterator currentInfo = additionalAtomData.begin();
+  for(std::map<const atomId_t, TremoloAtomInfoContainer>::iterator currentInfo = additionalAtomData.begin();
     currentInfo != additionalAtomData.end(); currentInfo++
   ) {
@@ -595 +590 @@
   }
 
-  for(map<int, TremoloAtomInfoContainer>::iterator currentInfo = additionalAtomData.begin();
+  for(std::map<const atomId_t, TremoloAtomInfoContainer>::iterator currentInfo = additionalAtomData.begin();
     currentInfo != additionalAtomData.end(); currentInfo++
   ) {
@@ -628 +623 @@
   knownTypes.clear();
 
-  LOG(3, "additionalAtomData contains: " << additionalAtomData);
+//  LOG(3, "INFO: additionalAtomData contains: " << additionalAtomData);
 
   // parse in file

src/Parser/TremoloParser.hpp

@@ -97 +97 @@
    * file.
    */
-  std::map<int, TremoloAtomInfoContainer> additionalAtomData;
+  std::map<const atomId_t, TremoloAtomInfoContainer> additionalAtomData;
 
   /**