Changeset dc1d9e for src/Parser

Timestamp:

Aug 28, 2010, 12:58:44 AM (15 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:

74a444

Parents:

1a7fd2

git-author:

Frederik Heber <heber@…> (08/27/10 22:17:27)

git-committer:

Frederik Heber <heber@…> (08/28/10 00:58:44)

Message:

Several bugfixes for TremoloParser.

• overloaded readAtomDataLine to also accept molecule*.
• BUGFIX: TremoloParser::writeNeighbors() and TremoloParser::saveLine() write ...->getId()+1.
• BUGFIX: TremoloParser::writeNeighbors() forgot to increase currentBond iterator.

Location:

src/Parser

Files:

• TremoloParser.cpp (modified) (7 diffs)
• TremoloParser.hpp (modified) (2 diffs)

src/Parser/TremoloParser.cpp

@@ -26 +26 @@
 #include "World.hpp"
 #include "atom.hpp"
+#include "bond.hpp"
 #include "element.hpp"
-#include "bond.hpp"
+#include "molecule.hpp"
 #include "periodentafel.hpp"
 #include "Descriptors/AtomIdDescriptor.hpp"
@@ -88 +89 @@
 
   usedFields.clear();
+  molecule *newmol = World::getInstance().createMolecule();
   while (file->good()) {
     std::getline(*file, line, '\n');
@@ -97 +99 @@
     }
     if (line.length() > 0 && line.at(0) != '#') {
-      readAtomDataLine(line);
+      readAtomDataLine(line, newmol);
     }
   }
@@ -169 +171 @@
         break;
       case TremoloKey::Id :
-        *file << currentAtom->getId() << "\t";
+        *file << currentAtom->getId()+1 << "\t";
         break;
       case TremoloKey::neighbors :
@@ -197 +199 @@
   for (int i = 0; i < numberOfNeighbors; i++) {
     *file << (currentBond != currentAtom->ListOfBonds.end()
-        ? (*currentBond)->GetOtherAtom(currentAtom)->getId() : 0) << "\t";
+        ? (*currentBond)->GetOtherAtom(currentAtom)->getId()+1 : 0) << "\t";
+    if (currentBond != currentAtom->ListOfBonds.end())
+      currentBond++;
   }
 }
@@ -229 +233 @@
  *
  * \param line to parse as an atom
- */
-void TremoloParser::readAtomDataLine(string line) {
+ * \param *newmol molecule to add atom to
+ */
+void TremoloParser::readAtomDataLine(string line, molecule *newmol = NULL) {
   vector<string>::iterator it;
   stringstream lineStream;
@@ -279 +284 @@
     }
   }
+  if (newmol != NULL)
+    newmol->AddAtom(newAtom);
 }
 

src/Parser/TremoloParser.hpp

@@ -11 +11 @@
 #include <string>
 #include "Parser/FormatParser.hpp"
+
+class molecule;
 
 /**
@@ -85 +87 @@
 private:
   void readAtomDataLine(string line);
+  void readAtomDataLine(string line, molecule *newmol);
   void parseAtomDataKeysLine(string line, int offset);
   void readNeighbors(std::stringstream* line, int numberOfNeighbors, int atomId);