stormm::structure::RMSDPlanReader< T > Struct Template Reference

Read-only abstract for the RMSDPlan object, containing pointers to various buckets of atom indices. More...

#include <rmsd_plan.h>

Collaboration diagram for stormm::structure::RMSDPlanReader< T >:

Public Member Functions
	RMSDPlanReader (int plan_count_in, RMSDMethod strategy_in, double mass_fraction_in, const T *masses_in, const int *atom_counts_in, const int *atom_starts_in, const int *alignment_steps_in, const int *core_atoms_in, const int *core_counts_in, const int *core_starts_in, const int *symm_atoms_in, const int4 *symm_bounds_in, const int2 *symm_ranges_in)
	The constructor takes inputs for all arguments.
	RMSDPlanReader (const RMSDPlanReader &original)
	The presence of const members will implicitly delete the copy and move assignment operators, but the default copy and move constructors will apply.
	RMSDPlanReader (RMSDPlanReader &&original)

Public Attributes
const int	plan_count
	The number of individual system RMSD calculation plans.
const RMSDMethod	strategy
const double	mass_fraction
const T *	masses
	Masses of particles in all systems.
const int *	atom_counts
	Numbers of atoms involved in the systems served by each plan.
const int *	atom_starts
const int *	alignment_steps
	Protocols for performing RMSD calculations under each plan.
const int *	core_atoms
	Concatenated lists of asymmetric atoms in each system.
const int *	core_counts
const int *	core_starts
const int *	symm_atoms
	Concatenated lists of each system's symmetry-related atoms.
const int4 *	symm_bounds
const int2 *	symm_ranges

Detailed Description

template<typename T>
struct stormm::structure::RMSDPlanReader< T >

Read-only abstract for the RMSDPlan object, containing pointers to various buckets of atom indices.

Member Data Documentation

atom_starts

template<typename T>

const int* stormm::structure::RMSDPlanReader< T >::atom_starts

Starting positions of the atom series associated with each plan (each plan pertains to a unique topology)

core_counts

template<typename T>

const int* stormm::structure::RMSDPlanReader< T >::core_counts

Exact numbers of asymmetric atoms in each system (each system's core atom list is padded by the warp size)

core_starts

template<typename T>

const int* stormm::structure::RMSDPlanReader< T >::core_starts

Bounds array for core_atoms, above (use this for offsets, and core counts for exact counts

mass_fraction

template<typename T>

const double stormm::structure::RMSDPlanReader< T >::mass_fraction

Total mass fraction needed to provide a critical alignment for subsequent determination of symmetry-related atom groups

strategy

template<typename T>

const RMSDMethod stormm::structure::RMSDPlanReader< T >::strategy

RMSD calculations are mass- or coordinate-weighted, aligned or not

symm_bounds

template<typename T>

const int4* stormm::structure::RMSDPlanReader< T >::symm_bounds

Bounds for symmetry-related atom group lists in the symm_atoms array. The "x" and "y" members list the lower and upper limits of all symmetry-related domains in each group, while the "z" members list the domain size and the "w" member gives the total number of domains.

symm_ranges

template<typename T>

const int2* stormm::structure::RMSDPlanReader< T >::symm_ranges

Bounds array on the symmetric atom bounds array–indicating the lower and upper limits of symmetric atom numbered groups in each system in the "x" and "y" members of each tuple.

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The documentation for this struct was generated from the following file:

• src/Structure/rmsd_plan.h