A class to merge two sets of CMAP surfaces. While the AtomGraphSynthesis has a means for doing this, it is more advanced and fits in the context of a different data structure. Similar ideas will be applied in the limited case of finding the union of two parameter sets. More...

#include <atomgraph_refinement.h>

Public Member Functions
int	getUniqueSurfaceCount () const
	Get the number of unique CMAP surfaces.

int	getContributingTopologyCount () const
	Get the number of contributing topologies.

std::vector< double >	getCmapSurface (int surf_index) const
	Get a CMAP surface based on its index in the consensus parameter set.

const std::vector< double > &	getAllSurfaces () const
	Get a vector of all surfaces in the union.

void	addSet (const double surf_v, const int dim_v, int nmap, double tol=constants::small)
	Add another set of CMAP terms to the union.


	CmapSurfaceUnion ()
	Rather than take ValenceKit abstracts and introduce a dependency on atomgraph_abstracts.h, the constructor cherry-picks the relevant details from each valence interaction abstract of the two topologies.

	CmapSurfaceUnion (const double surf_a, const int dim_a, int nmap_a, const double surf_b, const int dim_b, int nmap_b, double match_tol=constants::small)

	CmapSurfaceUnion (const double surf_a, const int dim_a, int nmap_a)

	CmapSurfaceUnion (const std::vector< double > &surf_a, const std::vector< int > &dim_a, const std::vector< double > &surf_b, const std::vector< int > &dim_b, double match_tol=constants::small)

	CmapSurfaceUnion (const std::vector< double > &surf_a, const std::vector< int > &dim_a)


	CmapSurfaceUnion (const CmapSurfaceUnion &orig)=default
	With only Standard Template Library elements for arrays and scalar member variables otherwise, the default copy and move constructors as well as the copy and move assignment operators will be adequate.

	CmapSurfaceUnion (CmapSurfaceUnion &&orig)=default

CmapSurfaceUnion &	operator= (const CmapSurfaceUnion &orig)=default

CmapSurfaceUnion &	operator= (CmapSurfaceUnion &&orig)=default


const std::vector< int > &	getSurfaceDimensions () const
	Get the dimension of one or all surfaces in the consensus parameter set. Each CMAP surface is assumed to be a square grid.

int	getSurfaceDimensions (int surf_index) const


const std::vector< int > &	getCorrespondence (int set_index) const
	Access the CMAP surface parameter index correspondence for a particular input set (input sets will, for most purposes, be specific topologies).

int	getCorrespondence (int set_index, int surf_index) const

Detailed Description

A class to merge two sets of CMAP surfaces. While the AtomGraphSynthesis has a means for doing this, it is more advanced and fits in the context of a different data structure. Similar ideas will be applied in the limited case of finding the union of two parameter sets.

Constructor & Destructor Documentation

◆ CmapSurfaceUnion() [1/2]

stormm::topology::CmapSurfaceUnion::CmapSurfaceUnion ( )

Rather than take ValenceKit abstracts and introduce a dependency on atomgraph_abstracts.h, the constructor cherry-picks the relevant details from each valence interaction abstract of the two topologies.

Overloaded:

Initialize an empty object
Provide the data as raw, C-style arrays
Provide the data as Standard Template Library vectors

Parameters

surf_a	Concatenated array of CMAP surface values for the first topology
dim_a	Dimensions of the CMAP surfaces for the first topology (all surfaces are assumed to be square grids). Summing the squares of the elements of dim_a, as is done internally, provides a prefix sum indicating the bounds of each unique CMAP surface.
nmap_a	The number of distinct CMAP surfaces in the first topology, the trusted length of dim_a
surf_b	Concatenated array of CMAP surface values for the second topology
dim_b	Dimensions of the CMAP surfaces for the second topology
nmap_b	The number of distinct CMAP surfaces in the second topology
match_tol	The tolerance for declaring that the values at two points of different CMAPs are identical. All points on both surfaces must align to within this tolerance in order for the surfaces to be considered a match.

◆ CmapSurfaceUnion() [2/2]

stormm::topology::CmapSurfaceUnion::CmapSurfaceUnion ( const CmapSurfaceUnion & orig )

default

With only Standard Template Library elements for arrays and scalar member variables otherwise, the default copy and move constructors as well as the copy and move assignment operators will be adequate.

Parameters

original	The original object to copy or move
other	Another object placed on the right hand side of an assignment statement

Member Function Documentation

◆ addSet()

void stormm::topology::CmapSurfaceUnion::addSet	(	const double *	surf_v,
		const int *	dim_v,
		int	nmap,
		double	tol = constants::small )

Add another set of CMAP terms to the union.

Parameters

surf_v	The CMAP surface values with which to populate the object, concatenated
dims_v	The dimensions of each surface
nmap	The number of distinct CMAP surfaces
tol	The tolerance for declaring that the values at two points of different CMAPs are identical. All points on both surfaces must align to within this tolerance in order for the surfaces to be considered a match.

◆ getCmapSurface()

std::vector< double > stormm::topology::CmapSurfaceUnion::getCmapSurface ( int surf_index ) const

Get a CMAP surface based on its index in the consensus parameter set.

Parameters

surf_index The index of the surface of interest, with a count beginning at zero

◆ getCorrespondence()

const std::vector< int > & stormm::topology::CmapSurfaceUnion::getCorrespondence ( int set_index ) const

Access the CMAP surface parameter index correspondence for a particular input set (input sets will, for most purposes, be specific topologies).

Overloaded:

Provide the CMAP index within the topology of interest to get its index in the consensus
Provide only an indication of the topology to get the mapping for all of its CMAP parameters onto the consensus table

Parameters

set_index	Index of the topology of interest
surf_index	Index of the surface of interest within its native topology

◆ getSurfaceDimensions()

const std::vector< int > & stormm::topology::CmapSurfaceUnion::getSurfaceDimensions ( ) const

Get the dimension of one or all surfaces in the consensus parameter set. Each CMAP surface is assumed to be a square grid.

Overloaded:

Get all surface dimensions by providing no argument
Get a specific CMAP's dimension by specifying a parameter index

Parameters

surf_index The index of the CMAP surface of interest

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

src/Topology/atomgraph_refinement.h
src/Topology/atomgraph_refinement.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ CmapSurfaceUnion() [1/2]

◆ CmapSurfaceUnion() [2/2]

Member Function Documentation

◆ addSet()

◆ getCmapSurface()

◆ getCorrespondence()

◆ getSurfaceDimensions()