BALL::MolmecSupport Namespace Reference

Enumerations
Enums
enum	PairListAlgorithmType { HASH_GRID, BRUTE_FORCE }

Functions
BALL_EXPORT BALL::Size	calculateNonBondedAtomPairs (ForceField::PairVector &pair_vector, const AtomVector &atom_vector, const SimpleBox3 &box, double distance, bool periodic_boundary_enabled, PairListAlgorithmType type) throw (Exception::OutOfMemory)
BALL_EXPORT Size	sortNonBondedAtomPairsAfterSelection (ForceField::PairVector &pair_vector)
BALL_EXPORT BALL::Size	addNonOverlappingMolecules (System &system, const HashGrid3< const Atom * > &solute_grid, const System &solvent, const SimpleBox3 &box, double distance)
BALL_EXPORT void	adaptWaterBox (System &system, const SimpleBox3 &box)
BALL_EXPORT void	calculateMinimumImage (Vector3 &distance, const Vector3 &period)
template<typename TorsionType , typename AtomIteratorType >
Size	computeTorsions (const AtomIteratorType &start, const AtomIteratorType &end, std::vector< TorsionType > &torsions, bool use_selection=false)

Detailed Description

MolmecSupport

Enumeration Type Documentation

enum BALL::MolmecSupport::PairListAlgorithmType

The type of algorithm used to calculate the pair list.

Enumerator
HASH_GRID	use a hash grid
BRUTE_FORCE	brute force all against all

Definition at line 60 of file support.h.

Function Documentation

BALL_EXPORT void BALL::MolmecSupport::adaptWaterBox	(	System &	system,
		const SimpleBox3 &	box
	)

Adapt periodic water (or general solvent) boxes to our periodic boundary definition. Periodic water boxes created by different programs might contain molecules which have their center of gravity outside of the box because of a different defintion of the periodic boundary. This function adapts such boxes to our definition by simply translating such molecules to the opposite boundary wall such that their center of gravity lies in the box afterwards.

This might be obsoleted by PeriodicBoundarry::updateMolecules()

Parameters

system	the system containing the water box which is to be adapted
box	the box definition for the periodic boundary

BALL_EXPORT BALL::Size BALL::MolmecSupport::addNonOverlappingMolecules	(	System &	system,
		const HashGrid3< const Atom * > &	solute_grid,
		const System &	solvent,
		const SimpleBox3 &	box,
		double	distance
	)

Merge the non-overlapping molecules of a system into another system. Fills system with copies of the solvent molecules stored in solvent. Solvent molecules are added to system if the molecules lie in the box and if they do not overlap with the molecules in solute_grid. A molecule has an overlap with another molecule if any atom of the first molecule is within distance of any atom of the other molecule.

Parameters

system	the system to be filled
solute_grid	a hash grid containing the solute molecules
solvent	the system containing the solvent
box	the periodic boundary of system
distance	used to determine overlaps between two atoms

Returns

the number of molecules added to system

BALL_EXPORT void BALL::MolmecSupport::calculateMinimumImage	(	Vector3 &	distance,
		const Vector3 &	period
	)

Compute the minimum image

BALL_EXPORT BALL::Size BALL::MolmecSupport::calculateNonBondedAtomPairs	(	ForceField::PairVector &	pair_vector,
		const AtomVector &	atom_vector,
		const SimpleBox3 &	box,
		double	distance,
		bool	periodic_boundary_enabled,
		PairListAlgorithmType	type
	)
throw	(	Exception::OutOfMemory
	)

Create a pair vector for non-bonded interactions. Calculates a vector of atom pairs whose distance is smaller than distance. The type determines if a brute force algorithm (type == BRUTE_FORCE) or a more sophisticated grid method (type == HASH_GRID) is used.

Parameters

pair_vector	the vector containing pairs of interacting atoms
atom_vector	the atoms to be considered for pairs
box	the periodic boundary used (if periodic_boundary_enabled == true)
distance	the maximum distance (cut-off distance) for two atoms
periodic_boundary_enabled	flag indicating the use of periodic boundary conditions
type	the type of algorithm used to calculate the pair vector

Returns

the number of pairs generated (pair_vector.size())

template<typename TorsionType , typename AtomIteratorType >

Size BALL::MolmecSupport::computeTorsions	(	const AtomIteratorType &	start,
		const AtomIteratorType &	end,
		std::vector< TorsionType > &	torsions,
		bool	use_selection = false
	)

Compute all torsions in a given set of molecules.

Returns

the number of torsions added to torsions

Parameters

start	an iterator pointing to the start of the atoms
end	a past-the-end iterator for the atoms
torsions	the vector of torsions
use_selection	if set to true, a torsion will be added only if all four atoms are selected

Definition at line 154 of file support.h.

BALL_EXPORT Size BALL::MolmecSupport::sortNonBondedAtomPairsAfterSelection

(

ForceField::PairVector &

pair_vector

)

Sort the pair list. The atom pairs in the list ar sorted in such a way, that those atom pairs where at least one of the atoms is selected are at the beginning of the list. The number of such pairs is returned. Running time is linear in the length of the list.

Returns

number of atom pairs in the list, where at least one atom is selected

Parameters

pair_vector

the unsorted pair_list (modified during the sorting)