Ignore:
Timestamp:
Aug 28, 2010, 12:57:56 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, Candidate_v1.7.1, 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:
21585f
Parents:
5c6946
git-author:
Frederik Heber <heber@…> (08/27/10 10:37:13)
git-committer:
Frederik Heber <heber@…> (08/28/10 00:57:56)
Message:

Added PdbParser with save capability.

  • load does not yet work.
  • added test part to Simple_configuration/2 (new file test.pdb)
File:
1 edited

Legend:

Unmodified
Added
Removed

  • src/Parser/PdbParser.hpp

    r5c6946 rbb6193  
    1313
    1414/**
    15  * Known keys for the ATOMDATA line.
     15 * Known keys for the Pdb line.
    1616 */
    17 class TremoloKey {
     17class PdbKey {
    1818public:
    19   enum atomDataKey {
     19  enum PdbDataKey {
    2020    noKey,
    2121    x,
    22     u,
    23     F,
    24     stress,
    2522    Id,
    26     neighbors,
    27     imprData,
    28     GroupMeasureTypeNo,
    2923    Type,
    3024    extType,
    … …  
    3630    tempFactor,
    3731    segID,
    38     Charge,
    39     charge,
    40     GrpTypeNo,
    41     torsion
     32    charge
    4233  };
    4334};
    … …  
    4637 * Holds tremolo-specific information which is not store in the atom class.
    4738 */
    48 class TremoloAtomInfoContainer {
     39class PdbAtomInfoContainer {
    4940public:
    50   TremoloAtomInfoContainer();
    51   void set(TremoloKey::atomDataKey key, std::string value);
    52   std::string get(TremoloKey::atomDataKey key);
    53   std::string F;
    54   std::string stress;
    55   std::string imprData;
    56   std::string GroupMeasureTypeNo;
     41  PdbAtomInfoContainer();
     42  void set(PdbKey::PdbDataKey key, std::string value);
     43  std::string get(PdbKey::PdbDataKey key);
     44  std::string name;
    5745  std::string extType;
    58   std::string name;
    5946  std::string resName;
    6047  std::string chainID;
    … …  
    6350  std::string tempFactor;
    6451  std::string segID;
    65   std::string Charge;
    6652  std::string charge;
    67   std::string GrpTypeNo;
    68   std::string torsion;
    69   std::vector<int> neighbors;
    7053};
    7154
    … …  
    8063  void load(std::istream* file);
    8164  void save(std::ostream* file);
    82   void setFieldsForSave(std::string atomDataLine);
    8365
    8466
    … …  
    9375  bool isUsedField(std::string fieldName);
    9476  void writeNeighbors(std::ostream* file, int numberOfNeighbors, atom* currentAtom);
    95   void saveLine(std::ostream* file, atom* currentAtom);
     77  void saveLine(ostream* file, const atom* currentAtom, const char *name, const int AtomNo, const int ResdueNo);
     78;
    9679
    9780  /**
    9881   * Map to associate the known keys with numbers.
    9982   */
    100   std::map<std::string, TremoloKey::atomDataKey> knownKeys;
    101 
    102   /**
    103    * Fields used in the tremolo file.
    104    */
    105   std::vector<std::string> usedFields;
     83  std::map<std::string, PdbKey::PdbDataKey> knownKeys;
    10684
    10785  /**
    … …  
    10987   * file.
    11088   */
    111   std::map<int, TremoloAtomInfoContainer> additionalAtomData;
     89  std::map<int, PdbAtomInfoContainer> additionalAtomData;
    11290
    11391  /**
    11492   * Default additional atom data.
    11593   */
    116   TremoloAtomInfoContainer defaultAdditionalData;
     94  PdbAtomInfoContainer defaultAdditionalData;
    11795
    11896  /**
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