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
Rev | Line | |
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[7d5fcd] | 1 | /*
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| 2 | * SaturatedFragment.hpp
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| 3 | *
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| 4 | * Created on: Mar 3, 2013
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| 5 | * Author: heber
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| 6 | */
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| 7 |
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| 8 | #ifndef SATURATEDFRAGMENT_HPP_
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| 9 | #define SATURATEDFRAGMENT_HPP_
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| 10 |
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| 11 | // include config.h
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| 12 | #ifdef HAVE_CONFIG_H
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| 13 | #include <config.h>
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| 14 | #endif
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| 15 |
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| 16 | #include <set>
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| 17 |
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| 18 | #include "Fragmentation/KeySet.hpp"
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| 19 |
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| 20 | class HydrogenPool;
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| 21 |
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| 22 | /** The SaturatedFragment class acts as a wrapper to a KeySet by adding a list
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| 23 | * of saturation hydrogens.
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| 24 | *
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| 25 | * This SaturatedFragment along with a currently leased set of hydrogens from the
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| 26 | * HydrogenPool is all that is required to create a fully storable molecular
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| 27 | * fragment from a given Keyset.
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| 28 | *
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| 29 | * The instance notes down its existence in an external container.
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| 30 | *
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| 31 | */
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| 32 | class SaturatedFragment
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| 33 | {
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| 34 | public:
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| 35 | //!> typedef to a container to mark keysets that are in use
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| 36 | typedef std::set<KeySet> KeySetsInUse_t;
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| 37 |
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| 38 | /** Constructor of SaturatedFragment requires \a set which we are tightly
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| 39 | * associated.
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| 40 | *
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| 41 | * \param _set KeySet which this instance is associated with
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| 42 | * \param _container container to add KeySet as in-use
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| 43 | * \param _hydrogens pool with hydrogens for saturation
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| 44 | */
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| 45 | SaturatedFragment(
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| 46 | const KeySet &_set,
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| 47 | KeySetsInUse_t &_container,
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| 48 | HydrogenPool &_hydrogens);
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| 49 |
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| 50 | /** Destructor of class SaturatedFragment.
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| 51 | *
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| 52 | */
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| 53 | ~SaturatedFragment();
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| 54 |
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| 55 | /** Getter for the KeySet this instance is associated with.
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| 56 | *
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| 57 | * \return const ref to KeySet
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| 58 | */
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| 59 | const KeySet & getKeySet() const
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| 60 | {
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| 61 | return set;
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| 62 | }
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| 63 |
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| 64 | private:
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| 65 | //!> container to mark ourselves RAII-style
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| 66 | KeySetsInUse_t &container;
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| 67 | //!> key set this fragment is associated with.
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| 68 | const KeySet &set;
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| 69 | //!> pool with saturation hydrogens
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| 70 | HydrogenPool &hydrogens;
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| 71 | //!> key set containing all atoms used for e.g. storing this to file
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| 72 | KeySet FullMolecule;
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| 73 | //!> key set containing the ids of all hydrogens added for saturation
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| 74 | KeySet SaturationHydrogens;
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| 75 | };
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| 76 |
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| 77 | #endif /* SATURATEDFRAGMENT_HPP_ */
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