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 63839f was             ad011c, checked in by Frederik Heber <heber@…>, 15 years ago           | 
        
        
          | 
             
CodePatterns places all includes now in subfolder CodePatterns/. 
 
- change all includes accordingly.
 - this was necessary as Helpers and Patterns are not very distinctive names
for include folders. Already now, we had a conflict between Helpers from
CodePatterns and Helpers from this project.
 - changed compilation test in ax_codepatterns.m4 when changing CodePatterns includes.
  
           | 
        
        
          
            
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 set to                 
100644
               
             
           | 
        
        
          | 
            File size:
            2.2 KB
           | 
        
      
      
| Rev | Line |   | 
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| [bcf653] | 1 | /*
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 | 2 |  * Project: MoleCuilder
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 | 3 |  * Description: creates and alters molecular systems
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 | 4 |  * Copyright (C)  2010 University of Bonn. All rights reserved.
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 | 5 |  * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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 | 6 |  */
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 | 7 | 
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| [97ebf8] | 8 | /*
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 | 9 |  * SaveBondsAction.cpp
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 | 10 |  *
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 | 11 |  *  Created on: May 10, 2010
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 | 12 |  *      Author: heber
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 | 13 |  */
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 | 14 | 
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| [bf3817] | 15 | // include config.h
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 | 16 | #ifdef HAVE_CONFIG_H
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 | 17 | #include <config.h>
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 | 18 | #endif
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 | 19 | 
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| [ad011c] | 20 | #include "CodePatterns/MemDebug.hpp"
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| [112b09] | 21 | 
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| [1a3c26] | 22 | #include "bondgraph.hpp"
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 | 23 | #include "config.hpp"
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| [ad011c] | 24 | #include "CodePatterns/Log.hpp"
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| [1a3c26] | 25 | #include "molecule.hpp"
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| [ad011c] | 26 | #include "CodePatterns/Verbose.hpp"
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| [1a3c26] | 27 | #include "World.hpp"
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 | 28 | 
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| [97ebf8] | 29 | 
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 | 30 | #include <iostream>
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 | 31 | #include <fstream>
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 | 32 | #include <string>
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 | 33 | 
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 | 34 | using namespace std;
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 | 35 | 
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| [1fd675] | 36 | #include "Actions/MoleculeAction/SaveBondsAction.hpp"
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| [fdf198] | 37 | 
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| [1fd675] | 38 | // and construct the stuff
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 | 39 | #include "SaveBondsAction.def"
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 | 40 | #include "Action_impl_pre.hpp"
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 | 41 | /** =========== define the function ====================== */
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| [97ebf8] | 42 | Action::state_ptr MoleculeSaveBondsAction::performCall() {
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 | 43 |   molecule *mol = NULL;
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 | 44 | 
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| [1fd675] | 45 |   // obtain information
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 | 46 |   getParametersfromValueStorage();
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| [97ebf8] | 47 | 
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| [fdf198] | 48 |   for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
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 | 49 |     mol = iter->second;
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| [1fd675] | 50 |     DoLog(0) && (Log() << Verbose(0) << "Storing bonds to path " << params.bondsfile << "." << endl);
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| [97ebf8] | 51 |     World::getInstance().getConfig()->BG->ConstructBondGraph(mol);
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| [35b698] | 52 |     // TODO: sollte stream, nicht filenamen direkt nutzen, besser fuer unit tests
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| [e4afb4] | 53 |     mol->StoreBondsToFile(params.bondsfile.leaf(), params.bondsfile.branch_path().string());
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| [97ebf8] | 54 |   }
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| [fdf198] | 55 |   return Action::success;
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| [97ebf8] | 56 | }
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 | 57 | 
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 | 58 | Action::state_ptr MoleculeSaveBondsAction::performUndo(Action::state_ptr _state) {
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 | 59 | //  MoleculeSaveBondsState *state = assert_cast<MoleculeSaveBondsState*>(_state.get());
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 | 60 | 
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 | 61 | //  string newName = state->mol->getName();
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 | 62 | //  state->mol->setName(state->lastName);
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 | 63 | 
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 | 64 |   return Action::failure;
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 | 65 | }
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 | 66 | 
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 | 67 | Action::state_ptr MoleculeSaveBondsAction::performRedo(Action::state_ptr _state){
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 | 68 |   // Undo and redo have to do the same for this action
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 | 69 |   return performUndo(_state);
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 | 70 | }
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 | 71 | 
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 | 72 | bool MoleculeSaveBondsAction::canUndo() {
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 | 73 |   return false;
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 | 74 | }
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 | 75 | 
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 | 76 | bool MoleculeSaveBondsAction::shouldUndo() {
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 | 77 |   return false;
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 | 78 | }
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| [1fd675] | 79 | /** =========== end of function ====================== */
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