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
      
      
      
| Line |  | 
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| 1 | /* | 
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| 2 | * Project: MoleCuilder | 
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| 3 | * Description: creates and alters _atomecular systems | 
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| 4 | * Copyright (C)  2010-2012 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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| 8 | /* | 
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| 9 | * AtomOrderDescriptor.cpp | 
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| 10 | * | 
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| 11 | *  Created on: Mar 22, 2012 | 
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| 12 | *      Author: heber | 
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| 13 | */ | 
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| 14 |  | 
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| 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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| 20 | #include "CodePatterns/MemDebug.hpp" | 
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| 21 |  | 
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| 22 | #include "AtomOrderDescriptor.hpp" | 
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| 23 | #include "AtomOrderDescriptor_impl.hpp" | 
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| 24 |  | 
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| 25 | #include "Atom/atom.hpp" | 
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| 26 | #include "CodePatterns/Observer/ObservedContainer_impl.hpp" | 
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| 27 |  | 
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| 28 | using namespace std; | 
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| 29 |  | 
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| 30 |  | 
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| 31 | AtomOrderDescriptor_impl::AtomOrderDescriptor_impl(int _id) : | 
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| 32 | id(_id) | 
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| 33 | {} | 
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| 34 |  | 
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| 35 | AtomOrderDescriptor_impl::~AtomOrderDescriptor_impl() | 
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| 36 | {} | 
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| 37 |  | 
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| 38 | bool AtomOrderDescriptor_impl::predicate(std::pair<atomId_t,atom*> _atom) | 
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| 39 | { | 
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| 40 | atom *Walker = find(); | 
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| 41 | return (Walker == _atom.second); | 
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| 42 | } | 
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| 43 |  | 
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| 44 | AtomDescriptor AtomByOrder(int id){ | 
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| 45 | return AtomDescriptor(AtomDescriptor::impl_ptr(new AtomOrderDescriptor_impl(id))); | 
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| 46 | } | 
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| 47 |  | 
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| 48 | World::AtomSet& AtomOrderDescriptor_impl::getAtoms() | 
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| 49 | { | 
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| 50 | return World::getInstance().atoms; | 
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| 51 | } | 
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| 52 |  | 
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| 53 |  | 
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| 54 | atom *AtomOrderDescriptor_impl::find(){ | 
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| 55 | World::AtomSet &atoms = getAtoms(); | 
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| 56 |  | 
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| 57 | int i=0; | 
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| 58 | atom *_atom = NULL; | 
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| 59 | if (id == 0) { | 
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| 60 | return NULL; | 
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| 61 | } else if (id > 0) { | 
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| 62 | World::AtomSet::internal_iterator res = atoms.begin_internal(); | 
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| 63 | for (; res != atoms.end_internal(); ++res) { // when iterator is normal, ++ goes forward! | 
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| 64 | ++i; | 
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| 65 | if (id == i) { | 
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| 66 | _atom = res->second; | 
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| 67 | break; | 
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| 68 | } | 
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| 69 | } | 
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| 70 | } else { | 
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| 71 | World::AtomSet::reverse_internal_iterator res = atoms.rbegin_internal(); | 
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| 72 | for (; res != atoms.rend_internal(); ++res) {  // when iterator is reverse, ++ goes backward! | 
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| 73 | --i; | 
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| 74 | if (id == i) { | 
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| 75 | _atom = res->second; | 
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| 76 | break; | 
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| 77 | } | 
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| 78 | } | 
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| 79 | } | 
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| 80 |  | 
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| 81 | return _atom; | 
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| 82 | } | 
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| 83 |  | 
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| 84 | vector<atom*> AtomOrderDescriptor_impl::findAll(){ | 
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| 85 | atom *res = find(); | 
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| 86 | return (res)?(vector<atom*>(1,res)):(vector<atom*>()); | 
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| 87 | } | 
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