Base class for the MM methods (currently: SFAM and GAFF). More...

#include <MolecularMechanicsCalculator.h>

Inheritance diagram for Scine::MolecularMechanics::MolecularMechanicsCalculator:

Collaboration diagram for Scine::MolecularMechanics::MolecularMechanicsCalculator:

Public Member Functions
	MolecularMechanicsCalculator ()=default
	Default Constructor.

virtual	~MolecularMechanicsCalculator () override=default
	Default Destructor.

	MolecularMechanicsCalculator (const MolecularMechanicsCalculator &rhs)

std::unique_ptr < Utils::AtomCollection >	getStructure () const override
	Gets the molecular structure as a const Utils::AtomCollection&. More...

void	modifyPositions (Utils::PositionCollection newPositions) override
	Allows to modify the positions of the underlying Utils::AtomCollection. More...

const Utils::PositionCollection &	getPositions () const override
	Getter for the coordinates of the underlying Utils::AtomCollection.

void	setRequiredProperties (const Utils::PropertyList &requiredProperties) override
	Sets the properties to calculate. More...

Utils::PropertyList	getRequiredProperties () const override
	Getter for the properties to calculate.

Utils::PropertyList	possibleProperties () const override
	Returns the list of the possible properties to calculate.

Utils::Settings &	settings () override
	Accessor for the settings. More...

const Utils::Settings &	settings () const override
	Constant accessor for the settings. More...

Utils::Results &	results () override
	Accessor for the saved instance of Utils::Results. More...

const Utils::Results &	results () const override
	Constant accessor for the Utils::Results. More...

bool	supportsMethodFamily (const std::string &methodFamily) const override
	Whether the calculator supports a method family. More...

std::shared_ptr< Core::State >	getState () const final
	Implements Core::StateHandableObject::getState(). More...

void	loadState (std::shared_ptr< Core::State >) final
	Implements Core::StateHandableObject::loadState(). More...

const std::vector< double > &	atomicCharges () const
	Const accessor for the atomic charges.

const std::vector< std::list < int > > &	listsOfNeighbors () const
	Const accessor for the lists of neighbors (the connectivity of the molecular system).

bool	allowsPythonGILRelease () const override
	Whether the calculator has no underlying Python code and can therefore release the global interpreter lock in Python bindings.

Public Member Functions inherited from Scine::Utils::CloneInterface< Utils::Abstract< MolecularMechanicsCalculator >, Core::Calculator >
std::shared_ptr < Utils::Abstract < MolecularMechanicsCalculator > >	clone () const

Protected Attributes
std::unique_ptr< Utils::Settings >	settings_

Utils::AtomCollection	structure_

Utils::PropertyList	requiredProperties_

Utils::Results	results_

std::vector< std::list< int > >	listsOfNeighbors_

std::vector< double >	atomicCharges_

Detailed Description

Base class for the MM methods (currently: SFAM and GAFF).

Member Function Documentation

std::shared_ptr< Core::State > Scine::MolecularMechanics::MolecularMechanicsCalculator::getState ( ) const

final

Implements Core::StateHandableObject::getState().

Returns: std::shared_ptr<Core::State> The current state

std::unique_ptr< Utils::AtomCollection > Scine::MolecularMechanics::MolecularMechanicsCalculator::getStructure ( ) const

override

Gets the molecular structure as a const Utils::AtomCollection&.

Returns: a const Utils::AtomCollection&.

void Scine::MolecularMechanics::MolecularMechanicsCalculator::loadState ( std::shared_ptr< Core::State > )

final

Implements Core::StateHandableObject::loadState().

Parameters

state The new state.

void Scine::MolecularMechanics::MolecularMechanicsCalculator::modifyPositions ( Utils::PositionCollection newPositions )

override

Allows to modify the positions of the underlying Utils::AtomCollection.

Parameters

newPositions The new positions to be assigned to the underlying Utils::AtomCollection.

Utils::Results & Scine::MolecularMechanics::MolecularMechanicsCalculator::results ( )

override

Accessor for the saved instance of Utils::Results.

Returns: Utils::Results& The results of the previous calculation.

const Utils::Results & Scine::MolecularMechanics::MolecularMechanicsCalculator::results ( ) const

override

Constant accessor for the Utils::Results.

Returns: const Utils::Results& The results of the previous calculation.

void Scine::MolecularMechanics::MolecularMechanicsCalculator::setRequiredProperties ( const Utils::PropertyList & requiredProperties )

override

Sets the properties to calculate.

Parameters

requiredProperties A Utils::PropertyList, a sequence of bits that represent the properties that must be calculated.

Utils::Settings & Scine::MolecularMechanics::MolecularMechanicsCalculator::settings ( )

override

Accessor for the settings.

Returns: Utils::Settings& The settings.

const Utils::Settings & Scine::MolecularMechanics::MolecularMechanicsCalculator::settings ( ) const

override

Constant accessor for the settings.

Returns: const Utils::Settings& The settings.

bool Scine::MolecularMechanics::MolecularMechanicsCalculator::supportsMethodFamily ( const std::string & methodFamily ) const

override

Whether the calculator supports a method family.

Parameters

methodFamily Identifier for the method family.

Returns: Whether the calculator supports a method family.

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

src/Swoose/Swoose/MolecularMechanics/MolecularMechanicsCalculator.h
src/Swoose/Swoose/MolecularMechanics/MolecularMechanicsCalculator.cpp

Public Member Functions

Protected Attributes

Detailed Description

Member Function Documentation