Collaboration diagram for Scine::SwooseUtilities::SubsystemGenerator:

Public Member Functions
	SubsystemGenerator (const Utils::AtomCollection &fullStructure, const Utils::BondOrderCollection &bondOrders, FragmentAnalyzer &fragmentAnalyzer, double bondOrderThreshold, int maximumSubsystemSize, Core::Log &log, int randomSeed=42, double probabilityToDivideBond=1.0)
	Constructor. More...

Utils::AtomCollection	generateSubsystem (int centralAtomIndex, std::vector< int > &atomIndexMapping, double subsystemRadius)
	Generates a subsystem (fragment) from a given full system. More...

Constructor & Destructor Documentation

Scine::SwooseUtilities::SubsystemGenerator::SubsystemGenerator	(	const Utils::AtomCollection &	fullStructure,
		const Utils::BondOrderCollection &	bondOrders,
		FragmentAnalyzer &	fragmentAnalyzer,
		double	bondOrderThreshold,
		int	maximumSubsystemSize,
		Core::Log &	log,
		int	randomSeed = `42`,
		double	probabilityToDivideBond = `1.0`
	)

Constructor.

Parameters

fullStructure	The molecular system's full structure.
bondOrders	The bond order matrix of the full system.
fragmentAnalyzer	A reference to a FragmentAnalyzer class.
bondOrderThreshold	Threshold of which bond order to still consider as a bond.
maximumSubsystemSize	Maximum size of a subsystem. If a large subsystem is generated, a warning is printed.
log	The logger.
randomSeed	The random seed that is set in the constructor. Default: 42
probabilityToDivideBond	Probability to cleave a bond that is in principle cleavable. Default: 1.0

Member Function Documentation

Utils::AtomCollection Scine::SwooseUtilities::SubsystemGenerator::generateSubsystem	(	int	centralAtomIndex,
		std::vector< int > &	atomIndexMapping,
		double	subsystemRadius
	)

Generates a subsystem (fragment) from a given full system.

Parameters

centralAtomIndex	The index of the central atom around which the subsystem will be constructed.
atomIndexMapping	Vector of indices that correspond to the indices of the atoms inside the given fragment in the full system. It is given as a reference and updated. Therefore, it is usually provided to the function as an empty vector.
additionToRadius	Variable extra amount that is added to the base subsystem radius and is updated whenever necessary.

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