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
      
      
        
          | 
            Last change
 on this file since 0b3cbdf was             73916f, checked in by Frederik Heber <heber@…>, 15 years ago           | 
        
        
          | 
             
Extended FormatParser::save() to use vector<atom *> to save. 
 
- This is needed to make the save functions also work on selected atoms or
molecules only.
 - Within ParserCommonUnitTest, ParserTremoloUnitTest we create the vector by
calling World's getAllAtoms() (which would have been done before in the
specialized save() functions).
 - new functions in FormatParserStorage:
- saveSelectedAtoms().
 - saveSelectedMolecules().
 - saveWorld().
 
  - renamed ::get() and ::put() to ::load() and ::save() to have it more
consistent with underlying FormatParser functions and also to avoid
misinterpretation with all ::get...() functions.
  
           | 
        
        
          
            
              - 
Property                 mode
 set to                 
100644
               
             
           | 
        
        
          | 
            File size:
            1.5 KB
           | 
        
      
      
| Rev | Line |   | 
|---|
| [bcf653] | 1 | /*
 | 
|---|
 | 2 |  * Project: MoleCuilder
 | 
|---|
 | 3 |  * Description: creates and alters molecular systems
 | 
|---|
 | 4 |  * Copyright (C)  2010 University of Bonn. All rights reserved.
 | 
|---|
 | 5 |  * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
 | 
|---|
 | 6 |  */
 | 
|---|
 | 7 | 
 | 
|---|
| [ab4b55] | 8 | /*
 | 
|---|
 | 9 |  * FormatParser.cpp
 | 
|---|
 | 10 |  *
 | 
|---|
 | 11 |  *  Created on: Mar 1, 2010
 | 
|---|
 | 12 |  *      Author: metzler
 | 
|---|
 | 13 |  */
 | 
|---|
 | 14 | 
 | 
|---|
| [bf3817] | 15 | // include config.h
 | 
|---|
 | 16 | #ifdef HAVE_CONFIG_H
 | 
|---|
 | 17 | #include <config.h>
 | 
|---|
 | 18 | #endif
 | 
|---|
 | 19 | 
 | 
|---|
| [112b09] | 20 | #include "Helpers/MemDebug.hpp"
 | 
|---|
 | 21 | 
 | 
|---|
| [ab4b55] | 22 | #include "FormatParser.hpp"
 | 
|---|
| [9131f3] | 23 | #include <iostream>
 | 
|---|
| [ab4b55] | 24 | 
 | 
|---|
 | 25 | using namespace std;
 | 
|---|
 | 26 | 
 | 
|---|
 | 27 | /**
 | 
|---|
 | 28 |  * Constructor.
 | 
|---|
 | 29 |  */
 | 
|---|
| [cd5047] | 30 | FormatParser::FormatParser() :
 | 
|---|
| [97b825] | 31 |   Observer("FormatParser"),
 | 
|---|
 | 32 |   saveStream(NULL)
 | 
|---|
| [cd5047] | 33 | {
 | 
|---|
| [2f40c0e] | 34 |   ChangeTracker::getInstance().signOn(this);
 | 
|---|
| [ab4b55] | 35 | }
 | 
|---|
 | 36 | 
 | 
|---|
 | 37 | /**
 | 
|---|
 | 38 |  * Destructor.
 | 
|---|
 | 39 |  */
 | 
|---|
 | 40 | FormatParser::~FormatParser() {
 | 
|---|
| [2f40c0e] | 41 |   ChangeTracker::getInstance().signOff(this);
 | 
|---|
| [ab4b55] | 42 | }
 | 
|---|
 | 43 | 
 | 
|---|
 | 44 | /**
 | 
|---|
 | 45 |  * Update operation which can be invoked by the observable (which should be the
 | 
|---|
 | 46 |  * change tracker here).
 | 
|---|
 | 47 |  */
 | 
|---|
 | 48 | void FormatParser::update(Observable *publisher) {
 | 
|---|
 | 49 |   if (!saveStream) {
 | 
|---|
| [9131f3] | 50 |     cerr << "Please invoke setOstream() so the parser knows where to save the World's data." << endl;
 | 
|---|
 | 51 |     return;
 | 
|---|
| [ab4b55] | 52 |   }
 | 
|---|
 | 53 | 
 | 
|---|
| [73916f] | 54 |   std::vector<atom *> atoms = World::getInstance().getAllAtoms();
 | 
|---|
 | 55 |   save(saveStream, atoms);
 | 
|---|
| [ab4b55] | 56 | }
 | 
|---|
 | 57 | 
 | 
|---|
 | 58 | /**
 | 
|---|
 | 59 |  * The observable can tell when it dies.
 | 
|---|
 | 60 |  */
 | 
|---|
 | 61 | void FormatParser::subjectKilled(Observable *publisher) {}
 | 
|---|
 | 62 | 
 | 
|---|
 | 63 | 
 | 
|---|
 | 64 | /**
 | 
|---|
 | 65 |  * Sets the output stream for save, so the save() method can be invoked on update
 | 
|---|
 | 66 |  * automatically.
 | 
|---|
 | 67 |  *
 | 
|---|
 | 68 |  * \param ostream where to save the World's state
 | 
|---|
 | 69 |  */
 | 
|---|
 | 70 | void FormatParser::setOstream(ostream* output) {
 | 
|---|
 | 71 |   saveStream = output;
 | 
|---|
 | 72 | }
 | 
|---|
       
      
  Note:
 See   
TracBrowser
 for help on using the repository browser.