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
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 8de597 was 5e6534, checked in by Frederik Heber <heber@…>, 13 years ago |
Refactored transform_iterator out of class molecule as AtomIdSet.
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100644
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File size:
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1 | /*
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2 | * AtomIdSet.hpp
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3 | *
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4 | * Created on: Feb 21, 2012
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5 | * Author: heber
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6 | */
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7 |
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8 | #ifndef ATOMIDSET_HPP_
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9 | #define ATOMIDSET_HPP_
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10 |
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11 |
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12 | // include config.h
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13 | #ifdef HAVE_CONFIG_H
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14 | #include <config.h>
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15 | #endif
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16 |
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17 | #include <boost/iterator/transform_iterator.hpp>
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18 |
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19 | #include <set>
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20 | #include <vector>
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21 |
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22 | #include "types.hpp"
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23 |
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24 | class atom;
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25 | struct FromIdToAtom :
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26 | public std::unary_function<atom *, atomId_t>
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27 | {
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28 | atom * operator()(atomId_t id) const;
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29 | };
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30 |
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31 | /** AtomIdSet is a set of atomic ids that however behave as a set of atoms.
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32 | *
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33 | * This class represents an iterable set of atoms that is however only stored as
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34 | * ids internally.
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35 | */
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36 | class AtomIdSet
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37 | {
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38 | public:
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39 | typedef std::set<atomId_t> atomIdSet;
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40 | typedef boost::transform_iterator<FromIdToAtom, atomIdSet::iterator, atom *, atomId_t> iterator;
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41 | typedef boost::transform_iterator<FromIdToAtom, atomIdSet::const_iterator, const atom *, atomId_t const &> const_iterator;
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42 |
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43 | AtomIdSet(const atomIdSet &_atoms);
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44 | AtomIdSet(const std::vector<atom *> &_atoms);
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45 | AtomIdSet();
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46 | ~AtomIdSet();
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47 |
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48 | iterator begin();
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49 | const_iterator begin() const;
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50 | iterator end();
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51 | const_iterator end() const;
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52 | bool empty() const;
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53 | size_t size() const;
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54 | const_iterator find(const atom * const key) const;
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55 | const_iterator find(const atomId_t &id) const;
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56 | std::pair<iterator, bool> insert(const atom * const key);
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57 | std::pair<iterator, bool> insert(const atomId_t &id);
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58 | const_iterator erase(const_iterator &loc);
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59 | const_iterator erase(const atom * const key);
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60 | const_iterator erase(const atomId_t &id);
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61 |
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62 | /** Getter for internal set of atoms.
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63 | *
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64 | * @return set of atomic ids
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65 | */
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66 | const atomIdSet & getAtomIds() const {
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67 | return atoms;
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68 | }
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69 |
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70 | private:
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71 | //!> internal atoms stored by their ids
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72 | atomIdSet atoms;
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73 | };
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74 |
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75 |
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76 | #endif /* ATOMIDSET_HPP_ */
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