Changeset 001f8a for src/Parser/PdbParser.hpp

Timestamp:

Dec 5, 2010, 12:21:03 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, Candidate_v1.7.0, 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:

fd19ff

Parents:

f03705 (diff), cabb46 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'ExtendLoadSaveXyztoAnyFormatParser' into stable

File:

• src/Parser/PdbParser.hpp (modified) (4 diffs)

src/Parser/PdbParser.hpp

@@ -10 +10 @@
 
 #include <string>
-#include "Parser/FormatParser.hpp"
+#include "FormatParser.hpp"
+#include "PdbAtomInfoContainer.hpp"
+#include "PdbKey.hpp"
 
 /**
- * Known keys for the Pdb line.
- */
-class PdbKey {
-public:
-  enum PdbDataKey {
-    noKey,
-    x,
-    Id,
-    Type,
-    extType,
-    name,
-    resName,
-    chainID,
-    resSeq,
-    occupancy,
-    tempFactor,
-    segID,
-    charge
-  };
-};
-
-/**
- * Holds tremolo-specific information which is not store in the atom class.
- */
-class PdbAtomInfoContainer {
-public:
-  PdbAtomInfoContainer();
-  void set(PdbKey::PdbDataKey key, std::string value);
-  std::string get(PdbKey::PdbDataKey key);
-  std::string name;
-  std::string extType;
-  std::string resName;
-  std::string chainID;
-  std::string resSeq;
-  std::string occupancy;
-  std::string tempFactor;
-  std::string segID;
-  std::string charge;
-};
-
-/**
- * Loads a tremolo file into the World and saves the World as a tremolo file.
+ * Loads a PDB format 3.2 file into the World and saves the World as a PDB file.
  */
 class PdbParser : public FormatParser
@@ -64 +25 @@
   void save(std::ostream* file);
 
+  bool operator==(const PdbParser& b) const;
+  void printAtomInfo(const atom *newAtom) const;
 
 private:
-  void readAtomDataLine(string line);
+  enum PdbKey::KnownTokens getToken(string &line);
+  void readAtomDataLine(string &line, molecule *newmol);
   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);
+  void readNeighbors(std::string &line);
+//  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(ostream* file, const atom* currentAtom, const char *name, const int AtomNo, const int ResdueNo);
-  int getAtomId(int atomid) const;
-  void setAtomId(int localatomid, int atomid);
+
+  // internal getter and setter
+  size_t getSerial(const size_t atomid) const;
+  size_t getAtomId(const size_t atomid) const;
+  void setAtomId(const size_t localatomid, const size_t atomid);
 
   /**
    * Map to associate the known keys with numbers.
    */
-  std::map<std::string, PdbKey::PdbDataKey> knownKeys;
+  std::map<std::string, PdbKey::KnownTokens> knownTokens;
 
   /**
@@ -88 +54 @@
    * file.
    */
-  std::map<int, PdbAtomInfoContainer> additionalAtomData;
+  std::map<size_t, PdbAtomInfoContainer> additionalAtomData;
 
   /**
@@ -99 +65 @@
    * world.
    */
-  std::map<int, int> atomIdMap;
+  std::map<size_t, size_t> atomIdMap;
+
+  /**
+   * Maps original atom IDs received from the parsed file to atom IDs in the
+   * world.
+   */
+  std::set<size_t> SerialSet;
+
 };