Changeset bd2390 for src/Parser

Timestamp:

Oct 25, 2010, 2:36:18 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:

9784cf

Parents:

6f5dfe

git-author:

Frederik Heber <heber@…> (10/25/10 14:29:06)

git-committer:

Frederik Heber <heber@…> (10/25/10 14:36:18)

Message:

BUGFIX: new boost::filesystem led to non-parsing of files.

• BUGFIX: MapOfActions::TypeMap is not only important for set/queryCurrentValue but also for CommandLineParser.
  • CommandLineDialog::FileCommandLineQuery::handle() expects boost::filesystem::path
  • new validate for boost::filesystem::path
  • AddOptionsToParser was missing case for enum File
  • no enum File in TypeEnumMap
• BUGFIX: InputAction
  • now setting prefix for all parsers even if filename nor present
  • now always setting name of last inserted molecule in World::getInstance().getMolecules()
  • not returning Action::failure when not present, only when not has_filename()
• BUGFIX: PdbParser and TremoloParser were not inserting, but only creating a new molecule
• BUGFIX: TremoloParser::load() nad no ASSET(false) as it's not implemented.
• BUGFIX: as molId of 0 may occur, PdbParser::save() prints -1 for homeless atoms now
• TESTFIX: Simple_configuration/2/test.pdb has molnr of 0 instead of former 1 (see above)

Location:

src/Parser

Files:

• MpqcParser.cpp (modified) (1 diff)
• PcpParser.cpp (modified) (1 diff)
• PdbParser.cpp (modified) (2 diffs)
• TremoloParser.cpp (modified) (1 diff)

src/Parser/MpqcParser.cpp

@@ -49 +49 @@
 void MpqcParser::load(istream *file)
 {
-  DoeLog(0) && (Log() << Verbose(0) << "Not yet implemented" << endl) ;
+  // TODO: MpqcParser::load implementation
+  ASSERT(false, "Not implemented yet");
 }
 

src/Parser/PcpParser.cpp

@@ -355 +355 @@
   // 3. parse the molecule in
   molecule *mol = World::getInstance().createMolecule();
-  MoleculeListClass *molecules = World::getInstance().getMolecules();
-  molecules->insert(mol);
+  mol->ActiveFlag = true;
+  // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
+  World::getInstance().getMolecules()->insert(mol);
   LoadMolecule(mol, FileBuffer, World::getInstance().getPeriode(), FastParsing);
-  //mol->SetNameFromFilename(filename);
-  mol->ActiveFlag = true;
-  //MolList->insert(mol);
 
   // 4. dissect the molecule into connected subgraphs

src/Parser/PdbParser.cpp

@@ -74 +74 @@
  */
 void PdbParser::load(istream* file) {
+  // TODO: PdbParser::load implementation
+  ASSERT(false, "Not implemented yet");
 //  string line;
 //  string::size_type location;
@@ -132 +134 @@
       elementNo[Z] = (elementNo[Z]+1) % 100;   // confine to two digits
       const molecule *mol = (*atomIt)->getMolecule();
-      if (mol == NULL) {  // for homeless atoms, MolNo = 0 is reserved
-        MolNo = 0;
+      if (mol == NULL) {  // for homeless atoms, MolNo = -1 is reserved
+        MolNo = -1;
       } else {
         MolNo = mol->getId();

src/Parser/TremoloParser.cpp

@@ -92 +92 @@
   usedFields.clear();
   molecule *newmol = World::getInstance().createMolecule();
+  newmol->ActiveFlag = true;
+  // 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 (file->good()) {
     std::getline(*file, line, '\n');