Collect instructions for one or more systems (intend to work with any coordinate object, including the PhaseSpaceSynthesis) More...

#include <rmsd_plan.h>

Public Member Functions
int	getPlanCount () const
	Get the number of plans kept within this object.

int	getPlanIndex (int index, SystemGrouping organization) const
	Get the plan index applicable to a specific grouping of systems (this assumes that all systems in the group have a valid interpretation by a single plan, and if that is not the case the result will be undefined).

RMSDMethod	getGeneralStrategy () const
	Get the general, prescribed strategy for computing RMSDs.

double	getRequiredMassFraction () const
	Get the mass fraction required to test symmetry-related atom arrangements without specific alignments.

const AtomGraph *	getTopologyPointer (int plan_index) const
	Get one of the topology pointers used by the RMSD plan.

RMSDAlignmentProtocol	getAlignmentProtocol (int plan_index) const
	Get one of the alignment protocols.

const RMSDPlanReader< double >	dpData (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the read-only abstract of the system in double precision. The masses of particles are the only templated type.

const RMSDPlanReader< float >	spData (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the read-only abstract of the system in single precision. The masses of particles are the only templated type.

const PhaseSpaceSynthesis *	getCoordinateSynthesisPointer () const
	Get the coordinate synthesis pointer.

const SystemCache *	getCachePointer () const
	Get the system cache pointer.

const SynthesisCacheMap *	getSynthesisMapPointer () const
	Get a pointer to the map between the cache and the coordinate synthesis.


	RMSDPlan (RMSDMethod strategy_in=RMSDMethod::ALIGN_MASS, double rmf_in=default_required_mass_fraction, const PhaseSpaceSynthesis poly_ps_in=nullptr, const SystemCache sc_in=nullptr, const SynthesisCacheMap *scmap_in=nullptr)
	The constructor can take any number of AtomEquivalence objects and build plans from them. Topology pointers will be harvested from these objects and, if necessary, matched to topologies in a synthesis object in order to connect each system to the appropriate instruction set.

	RMSDPlan (const AtomGraph &ag_in, const CoordinateFrame &cf_in, RMSDMethod strategy_in=RMSDMethod::ALIGN_MASS, double rmf_in=default_required_mass_fraction, const GpuDetails &gpu=null_gpu, int low_mol_idx=0, int high_mol_idx=-1)

	RMSDPlan (const AtomEquivalence &eq_in, RMSDMethod strategy_in=RMSDMethod::ALIGN_MASS, double rmf_in=default_required_mass_fraction, const GpuDetails &gpu=null_gpu)

	RMSDPlan (const PhaseSpaceSynthesis *poly_ps_in, RMSDMethod strategy_in=RMSDMethod::ALIGN_MASS, double rmf_in=default_required_mass_fraction, const GpuDetails &gpu=null_gpu, int low_mol_idx=0, int high_mol_idx=-1)

	RMSDPlan (const PhaseSpaceSynthesis *poly_ps_in, const std::vector< AtomEquivalence > &eq_list_in, RMSDMethod strategy_in=RMSDMethod::ALIGN_MASS, double rmf_in=default_required_mass_fraction, const GpuDetails &gpu=null_gpu)

	RMSDPlan (const PhaseSpaceSynthesis &poly_ps_in, RMSDMethod strategy_in=RMSDMethod::ALIGN_MASS, double rmf_in=default_required_mass_fraction, const GpuDetails &gpu=null_gpu, int low_mol_idx=0, int high_mol_idx=-1)

	RMSDPlan (const PhaseSpaceSynthesis &poly_ps_in, const std::vector< AtomEquivalence > &eq_list_in, RMSDMethod strategy_in=RMSDMethod::ALIGN_MASS, double rmf_in=default_required_mass_fraction, const GpuDetails &gpu=null_gpu)

	RMSDPlan (const PhaseSpaceSynthesis poly_ps_in, const SystemCache sc_in, const SynthesisCacheMap *scmap_in, const RMSDMethod strategy_in=RMSDMethod::ALIGN_MASS, const double rmf_in=default_required_mass_fraction, const GpuDetails &gpu=null_gpu, const int low_mol_idx=0, const int high_mol_idx=-1)

	RMSDPlan (const PhaseSpaceSynthesis &poly_ps_in, const SystemCache &sc_in, const SynthesisCacheMap &scmap_in, const RMSDMethod strategy_in=RMSDMethod::ALIGN_MASS, const double rmf_in=default_required_mass_fraction, const GpuDetails &gpu=null_gpu, const int low_mol_idx=0, const int high_mol_idx=-1)


	RMSDPlan (const RMSDPlan &original)=default
	With no POINTER-kind Hybrid or pointers to its own member variables to repair, and no const members, the RMSDPlan can make use of default copy and move constructors as well as copy and move assignment operators.

	RMSDPlan (RMSDPlan &&original)=default

RMSDPlan &	operator= (const RMSDPlan &original)=default

RMSDPlan &	operator= (RMSDPlan &&original)=default


void	addSystemCache (const SystemCache sc, const SynthesisCacheMap scmap)
	Attach a SystemCache and map between the cache and the synthesis to the object.

void	addSystemCache (const SystemCache &sc, const SynthesisCacheMap &scmap)

Detailed Description

Collect instructions for one or more systems (intend to work with any coordinate object, including the PhaseSpaceSynthesis)

Constructor & Destructor Documentation

◆ RMSDPlan() [1/2]

stormm::structure::RMSDPlan::RMSDPlan	(	RMSDMethod	strategy_in = RMSDMethod::ALIGN_MASS,
		double	rmf_in = default_required_mass_fraction,
		const PhaseSpaceSynthesis *	poly_ps_in = nullptr,
		const SystemCache *	sc_in = nullptr,
		const SynthesisCacheMap *	scmap_in = nullptr )

The constructor can take any number of AtomEquivalence objects and build plans from them. Topology pointers will be harvested from these objects and, if necessary, matched to topologies in a synthesis object in order to connect each system to the appropriate instruction set.

Parameters

strategy_in	The type of RMSD calculations that this plan will guide
rmf_in	The required mass fraction that constitutes enough of the molecule to perform placement of small symmetric atom groups without further alignment calculations
ag_in	Topology for which to draw a positional RMSD computation plan
cf_in	Input coordinates (used for making the necessary AtomEquivalence objects if they are not supplied explicitly)
eq_in	Pre-computed breakdown of all symmetry-related atoms
poly_ps_in	PhaseSpaceSynthesis object for which to draw plans covering all systems. Topology pointers will be harvested from the object.
eq_list_in	List of symmetry-related atom breakdowns for all systems in poly_ps_in
gpu	Details of the GPU that will be used in computing RMSD values
low_mol_idx	Lower limit of molecules from the topology to assess for symmetry groups (this, and high_mol_idx, are only used if a single topology is provided for automatic deduction of symmetry groups)
high_mol_idx	Upper limit of molecules from the topology to assess for symmetry groups. The default of -1 indicates that only one molecule, indicated by the lower index, should be assessed.

◆ RMSDPlan() [2/2]

stormm::structure::RMSDPlan::RMSDPlan ( const RMSDPlan & original )

default

With no POINTER-kind Hybrid or pointers to its own member variables to repair, and no const members, the RMSDPlan can make use of default copy and move constructors as well as copy and move assignment operators.

Parameters

original	Another object to copy or move in constructing this one
other	The right-hand side object of an assignment

Member Function Documentation

◆ addSystemCache()

void stormm::structure::RMSDPlan::addSystemCache	(	const SystemCache *	sc,
		const SynthesisCacheMap *	scmap )

Attach a SystemCache and map between the cache and the synthesis to the object.

Overloaded:

Specify the cache and map by const pointer
Specify the cache and map by const reference

Parameters

sc	The system cache, reflecting user specified input coordinates and topologies
scmap	The map between the synthesis and the system cache

◆ dpData()

const RMSDPlanReader< double > stormm::structure::RMSDPlan::dpData ( HybridTargetLevel tier = HybridTargetLevel::HOST ) const

Get the read-only abstract of the system in double precision. The masses of particles are the only templated type.

Parameters

tier	Get pointers at the level of the CPU host or GPU device

◆ getAlignmentProtocol()

RMSDAlignmentProtocol stormm::structure::RMSDPlan::getAlignmentProtocol ( int plan_index ) const

Get one of the alignment protocols.

Parameters

plan_index The system / plan of interest

◆ getPlanIndex()

int stormm::structure::RMSDPlan::getPlanIndex	(	int	index,
		SystemGrouping	organization ) const

Get the plan index applicable to a specific grouping of systems (this assumes that all systems in the group have a valid interpretation by a single plan, and if that is not the case the result will be undefined).

Parameters

index	Index of the grouping from one of the internal lists
organization	The manner in which systems are grouped

◆ getTopologyPointer()

const AtomGraph * stormm::structure::RMSDPlan::getTopologyPointer ( int plan_index ) const

Get one of the topology pointers used by the RMSD plan.

Parameters

plan_index The system / plan of interest

◆ spData()

const RMSDPlanReader< float > stormm::structure::RMSDPlan::spData ( HybridTargetLevel tier = HybridTargetLevel::HOST ) const

Get the read-only abstract of the system in single precision. The masses of particles are the only templated type.

Parameters

tier	Get pointers at the level of the CPU host or GPU device

The documentation for this class was generated from the following files:

src/Structure/rmsd_plan.h
src/Structure/rmsd_plan.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ RMSDPlan() [1/2]

◆ RMSDPlan() [2/2]

Member Function Documentation

◆ addSystemCache()

◆ dpData()

◆ getAlignmentProtocol()

◆ getPlanIndex()

◆ getTopologyPointer()

◆ spData()