Changeset b8d4a3 for src/Parser/TremoloParser.hpp

Timestamp:

May 2, 2010, 4:47:18 PM (15 years ago)

Author:

Saskia Metzler <metzler@…>

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:

b9b604

Parents:

4415da

Message:

Tremolo format parser

File:

• src/Parser/TremoloParser.hpp (modified) (3 diffs)

src/Parser/TremoloParser.hpp

@@ -13 +13 @@
 
 /**
- * Holds tremolo-specific information which is not store in the atom class.
+ * Known keys for the ATOMDATA line.
  */
-class TremoloAtomInfoContainer {
+class TremoloKey {
 public:
-  TremoloAtomInfoContainer();
-  std::string F;
-  std::string stress;
-  std::string imprData;
-  std::string GroupMeasureTypeNo;
-  std::string extType;
-  std::string name;
-  std::string resName;
-  std::string chainID;
-  std::string resSeq;
-  std::string occupancy;
-  std::string tempFactor;
-  std::string segID;
-  std::string Charge;
-  std::string charge;
-  std::string GrpTypeNo;
-};
-
-/**
- * Loads a tremolo file into the World and saves the World as a tremolo file.
- */
-class TremoloParser:public FormatParser
-{
-public:
-  TremoloParser();
-  ~TremoloParser();
-  void load(std::istream* file);
-  void save(std::ostream* file);
-
-private:
-  void readAtomDataLine(string line);
-  void parseAtomDataKeysLine(string line, int offset);
-
-  /**
-   * Known keys for the ATOMDATA line.
-   */
   enum atomDataKey {
     noKey,
@@ -74 +38 @@
     Charge,
     charge,
-    GrpTypeNo
+    GrpTypeNo,
+    torsion
   };
+};
+
+/**
+ * Holds tremolo-specific information which is not store in the atom class.
+ */
+class TremoloAtomInfoContainer {
+public:
+  TremoloAtomInfoContainer();
+  void set(TremoloKey::atomDataKey key, std::string value);
+  std::string get(TremoloKey::atomDataKey key);
+  std::string F;
+  std::string stress;
+  std::string imprData;
+  std::string GroupMeasureTypeNo;
+  std::string extType;
+  std::string name;
+  std::string resName;
+  std::string chainID;
+  std::string resSeq;
+  std::string occupancy;
+  std::string tempFactor;
+  std::string segID;
+  std::string Charge;
+  std::string charge;
+  std::string GrpTypeNo;
+  std::string torsion;
+  std::vector<int> neighbors;
+};
+
+/**
+ * Loads a tremolo file into the World and saves the World as a tremolo file.
+ */
+class TremoloParser : public FormatParser
+{
+public:
+  TremoloParser();
+  ~TremoloParser();
+  void load(std::istream* file);
+  void save(std::ostream* file);
+  void setFieldsForSave(std::string atomDataLine);
+
+
+private:
+  void readAtomDataLine(string line);
+  void parseAtomDataKeysLine(string line, int offset);
+  void readNeighbors(std::stringstream* line, int numberOfNeighbors, int atomId);
+  void processNeighborInformation();
+  void adaptImprData();
+  void adaptTorsion();
+  std::string adaptIdDependentDataString(std::string data);
+  bool isUsedField(std::string fieldName);
+  void writeNeighbors(std::ostream* file, int numberOfNeighbors, atom* currentAtom);
+  void saveLine(std::ostream* file, atom* currentAtom);
 
   /**
    * Map to associate the known keys with numbers.
    */
-  std::map<std::string, atomDataKey> knownKeys;
+  std::map<std::string, TremoloKey::atomDataKey> knownKeys;
 
   /**
@@ -91 +109 @@
    * file.
    */
-  std::map<int, TremoloAtomInfoContainer> moreData;
+  std::map<int, TremoloAtomInfoContainer> additionalAtomData;
+
+  /**
+   * Default additional atom data.
+   */
+  TremoloAtomInfoContainer defaultAdditionalData;
+
+  /**
+   * Maps original atom IDs received from the parsed file to atom IDs in the
+   * world.
+   */
+  std::map<int, int> atomIdMap;
 };