Changeset bd2390 for src/Actions

Timestamp:

Oct 25, 2010, 2:36:18 PM (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:

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/Actions

Files:

• MapOfActions.cpp (modified) (3 diffs)
• MapOfActions.hpp (modified) (1 diff)
• WorldAction/InputAction.cpp (modified) (1 diff)

src/Actions/MapOfActions.cpp

@@ -191 +191 @@
   BV.zz = boost::lexical_cast<double>(components.at(5));
   v = boost::any(BoxValue(BV));
+}
+
+void validate(boost::any& v, const std::vector<std::string>& values, boost::filesystem::path *, int)
+{
+  boost::filesystem::path filename;
+  std::vector<std::string> components;
+
+  std::cout << "boost::filesystem::path validator used." << std::endl;
+
+  // split comma-separated values
+  if (values.size() != 1) {
+    cerr <<  "Not one file but " << components.size() << " given " << endl;
+    throw boost::program_options::validation_error("Unequal to one file given");
+  }
+  filename = values.at(0);
+  v = boost::any(boost::filesystem::path(filename));
 }
 
@@ -447 +463 @@
   TypeEnumMap[&typeid(bool)] = Boolean;
   TypeEnumMap[&typeid(int)] = Integer;
+  TypeEnumMap[&typeid(boost::filesystem::path)] = File;
   TypeEnumMap[&typeid(std::vector<int>)] = ListOfIntegers;
   TypeEnumMap[&typeid(double)] = Double;
@@ -1078 +1095 @@
               ;
             break;
+          case File:
+            ListRunner->second->add_options()
+              (getKeyAndShortForm(*OptionRunner).c_str(),
+                  po::value< boost::filesystem::path >(),
+                  getDescription(*OptionRunner).c_str())
+              ;
+            break;
           case Integer:
             ListRunner->second->add_options()

src/Actions/MapOfActions.hpp

@@ -138 +138 @@
   friend class MapOfActionsTest;
 public:
-  enum OptionTypes { None, Boolean, Integer, ListOfIntegers, Double, ListOfDoubles, String, ListOfStrings, Vector, ListOfVectors, Box, Molecule, ListOfMolecules, Atom, ListOfAtoms, Element, ListOfElements };
+  enum OptionTypes { None, Boolean, Integer, File, ListOfIntegers, Double, ListOfDoubles, String, ListOfStrings, Vector, ListOfVectors, Box, Molecule, ListOfMolecules, Atom, ListOfAtoms, Element, ListOfElements };
 
   // getter for the action descriptions and short forms

src/Actions/WorldAction/InputAction.cpp

@@ -49 +49 @@
 
   DoLog(0) && (Log() << Verbose(0) << "Config file given " << params.filename << "." << endl);
+  // using the filename as prefix for all parsers
+  std::string FilenameSuffix;
+  std::string FilenamePrefix;
+  if (params.filename.has_filename()) {
+    // get suffix
+    FilenameSuffix = params.filename.extension().substr(1); // remove the prefixed "."
+    FilenamePrefix = params.filename.stem();
+    DoLog(1) && (Log() << Verbose(1) << "Setting config file name prefix to " << FilenamePrefix << "." << endl);
+    FormatParserStorage::getInstance().SetOutputPrefixForAll(FilenamePrefix);
+  } else {
+    DoeLog(1) && (eLog() << Verbose(1) << "Input file does not have a suffix, cannot recognize format." << endl);
+    return Action::failure;
+  }
+
+  // parsing file if present
   if (!boost::filesystem::exists(params.filename)) {
     DoLog(1) && (Log() << Verbose(1) << "Specified config file " << params.filename << " not found." << endl);
-    return Action::failure;
+    // DONT FAIL: it's just empty and we use the name. // return Action::failure;
   } else {
     DoLog(1) && (Log() << Verbose(1) << "Specified config file found, parsing ... ");
-    if (params.filename.has_filename()) {
-      // get suffix
-      std::string FilenameSuffix = params.filename.extension();
-      std::string FilenamePrefix = params.filename.stem();
-      DoLog(1) && (Log() << Verbose(1) << "Setting config file name prefix to " << FilenamePrefix << "." << endl);
-      FormatParserStorage::getInstance().SetOutputPrefixForAll(FilenamePrefix);
 
-      // parse the file
-      test.open(params.filename);
-      FormatParserStorage::getInstance().get(test, FilenameSuffix);
-      test.close();
-//
-//      // set mol to first active molecule
-//      if (molecules->ListOfMolecules.size() != 0) {
-//        for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
-//          if ((*ListRunner)->ActiveFlag) {
-//            mol = *ListRunner;
-//            break;
-//          }
-//      }
-//      if (mol == NULL) {
-//        mol = World::getInstance().createMolecule();
-//        mol->ActiveFlag = true;
-//        molecules->insert(mol);
-//      }
-//      mol->SetNameFromFilename(params.filename.substr(0,params.filename.find('.')).c_str());
-      return Action::success;
-    } else {
-      DoeLog(1) && (eLog() << Verbose(1) << "Input file does not have a suffix, cannot recognize format." << endl);
-      return Action::failure;
-    }
+    // parse the file
+    test.open(params.filename);
+    FormatParserStorage::getInstance().get(test, FilenameSuffix);
+    test.close();
+
+    // set file name of last molecule
+    MoleculeList::const_iterator iter = World::getInstance().getMolecules()->ListOfMolecules.end();
+    iter--;
+    (*iter)->SetNameFromFilename(FilenamePrefix.c_str());
   }
+  return Action::success;
 }