Scine::MolecularMechanics::InteractionExclusion Class Reference

This class provides a framework to store exclusions of interactions between atoms. Such exclusions are required for the non-covalent interactions between bonded atoms or to eliminate contributions to the energy for the interaction between QM atoms in QM/MM. More...

#include <InteractionExclusion.h>

Inheritance diagram for Scine::MolecularMechanics::InteractionExclusion:

Collaboration diagram for Scine::MolecularMechanics::InteractionExclusion:

Public Member Functions
	InteractionExclusion (unsigned int nAtoms)
	Constructor. More...
void	setExclusions (const Eigen::SparseMatrix< bool > &excludedPairs)
	Setter for the exclusion matrix. More...
void	addExclusions (const Eigen::SparseMatrix< bool > &excludedPairs)
	Add new exclusions. More...
void	addExclusions (const IndexedStructuralTopology &topology)
	Add the exclusions encoded in the topology, e.g., 1-3 and 1-2 interactions. More...
const Eigen::SparseMatrix< bool > &	getExclusions ()
	Getter for the exclusions. More...
void	resetExclusions (unsigned int nAtoms)
	Resize the exclusion matrix to the given number of atoms and remove all existing exlcuions. More...

Detailed Description

This class provides a framework to store exclusions of interactions between atoms. Such exclusions are required for the non-covalent interactions between bonded atoms or to eliminate contributions to the energy for the interaction between QM atoms in QM/MM.

The exclusions are stored as a sparse matrix atom x atom of booleans. If the entry is true for two atoms, their interaction is excluded.

Constructor & Destructor Documentation

Scine::MolecularMechanics::InteractionExclusion::InteractionExclusion

(

unsigned int

nAtoms

)

Constructor.

Parameters

nAtoms

The number of atoms.

Note that the number of atoms may be changed later by calling resetExclusions(...).

Member Function Documentation

void Scine::MolecularMechanics::InteractionExclusion::addExclusions

(

const Eigen::SparseMatrix< bool > &

excludedPairs

)

Add new exclusions.

Parameters

excludedPairs

The exclusions.

void Scine::MolecularMechanics::InteractionExclusion::addExclusions

(

const IndexedStructuralTopology &

topology

)

Add the exclusions encoded in the topology, e.g., 1-3 and 1-2 interactions.

Parameters

topology

The topology.

const Eigen::SparseMatrix< bool > & Scine::MolecularMechanics::InteractionExclusion::getExclusions

(

)

Getter for the exclusions.

Returns

The exclusions.

void Scine::MolecularMechanics::InteractionExclusion::resetExclusions

(

unsigned int

nAtoms

)

Resize the exclusion matrix to the given number of atoms and remove all existing exlcuions.

Parameters

nAtoms

The new number of atoms.

void Scine::MolecularMechanics::InteractionExclusion::setExclusions

(

const Eigen::SparseMatrix< bool > &

excludedPairs

)

Setter for the exclusion matrix.

Parameters

excludedPairs

The exclusion matrix.

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

• src/Swoose/Swoose/MolecularMechanics/InteractionExclusion.h
• src/Swoose/Swoose/MolecularMechanics/InteractionExclusion.cpp