stormm::topology::Map1234 Class Reference

Another unguarded class to help in the construction of an AtomGraph's categorized non-bonded exclusion lists. More...

#include <atomgraph_refinement.h>

Public Member Functions
	Map1234 ()
	The constructor simply allocates memory, if dimensions are available.
	Map1234 (int natom_in, int nb11_count_in, int nb12_count_in, int nb13_count_in, int nb14_count_in)
void	addExclusions (const std::vector< int3 > &plus_excl, ExceptionResponse policy=ExceptionResponse::DIE)
	A means to add exclusions to the object post-hoc, after construction.
void	addExclusions (const std::vector< int2 > &plus_excl, ExceptionResponse policy=ExceptionResponse::DIE)
void	removeExclusions (const std::vector< int3 > &minus_excl, ExceptionResponse policy=ExceptionResponse::DIE)
	A means to remove exclusions from the object post-hoc, after construction. Overloading and descriptions of input parameters follow from addExclusions(), above, in addition to:
void	removeExclusions (const std::vector< int2 > &minus_excl, ExceptionResponse policy=ExceptionResponse::DIE)

Public Attributes
std::vector< int >	nb11_excl_bounds
std::vector< int >	nb11_excl_list
	1:1 exclusions list (double-counts all exclusions)
std::vector< int >	nb12_excl_bounds
	Bond exclusion bounds list for each atom.
std::vector< int >	nb12_excl_list
	Bonded exclusions (double-counts all exclusions)
std::vector< int >	nb13_excl_bounds
	Bond angle exclusion bounds list for each atom.
std::vector< int >	nb13_excl_list
	Bond angle exclusions (double-counts all exclusions)
std::vector< int >	nb14_excl_bounds
	1:4 exclusions bounds list for each atom
std::vector< int >	nb14_excl_list
	1:4 exclusions (double-counts all exclusions)

Detailed Description

Another unguarded class to help in the construction of an AtomGraph's categorized non-bonded exclusion lists.

Constructor & Destructor Documentation

Map1234()

stormm::topology::Map1234::Map1234

(

)

The constructor simply allocates memory, if dimensions are available.

Overloaded:

• Create an empty object
• Create an object with pre-allocated memory for each virtual site

Parameters

natom_in	The number of atoms in the system (for bounds arrays)
nb11_count_in	The (known) number of 1:1 non-bonded exclusions
nb12_count_in	The (known) number of 1:2 non-bonded exclusions
nb13_count_in	The (known) number of 1:3 non-bonded exclusions
nb14_count_in	The (known) number of 1:4 non-bonded exclusions

Member Function Documentation

addExclusions()

void stormm::topology::Map1234::addExclusions	(	const std::vector< int3 > &	plus_excl,
		ExceptionResponse	policy = ExceptionResponse::DIE )

A means to add exclusions to the object post-hoc, after construction.

Overloaded:

• Provide two-tuples of integers, indicating the topological atom indices in their "x" and "y" members. The order of all exclusions will be set as 1:2 (separated by one "bond").
• Provide three-tuples of integers, indicating the topological atom indices as in the first case and then the order of the exclusion (1, 2, 3, or 4) in the "z" member

Parameters

plus_excl	The list of exclusions to add
policy	The course of action to take in the event that exclusions to be added are already present. It is always an error to indicate an invalid order for an exclusion.

removeExclusions()

void stormm::topology::Map1234::removeExclusions	(	const std::vector< int3 > &	minus_excl,
		ExceptionResponse	policy = ExceptionResponse::DIE )

A means to remove exclusions from the object post-hoc, after construction. Overloading and descriptions of input parameters follow from addExclusions(), above, in addition to:

Parameters

minus_excl

The list of exclusions to remove

Member Data Documentation

nb11_excl_bounds

std::vector<int> stormm::topology::Map1234::nb11_excl_bounds

1:1 exclusion bounds list for each atom (needed for virtual sites and atoms with virtual sites)

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

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