core Directory Reference

Directory dependency graph for core:

Files
file	AngleRestraint.h [code]
	Angle restraint between three particles.
file	AngleTripletScore.h [code]
	A Score on the angle between three particles.
file	AttributeSingletonScore.h [code]
	A score based on the unmodified value of an attribute.
file	core/BallMover.h [code]
	A modifier which variables within a ball.
file	blame.h [code]
	Various important functionality for implementing decorators.
file	BoundingBox3DSingletonScore.h [code]
	Score particles based on a bounding box.
file	BoxSweepClosePairsFinder.h [code]
	Test all pairs of particles to find close pairs.
file	CentroidOfRefined.h [code]
	Set the coordinates of the particle to be the centroid of the refined particles.
file	ChecksScoreState.h [code]
	Turn checks on and off.
file	ChildrenRefiner.h [code]
	Return the hierarchy children of a particle.
file	ClosedCubicSpline.h [code]
	Closed cubic spline function.
file	ClosePairsFinder.h [code]
	A base class for algorithms to detect proximities.
file	ClosePairsPairScore.h [code]
	Apply a PairScore to close pairs.
file	core/ConjugateGradients.h [code]
	Simple conjugate gradients optimizer.
file	ConnectivityRestraint.h [code]
	Connectivity restraint.
file	ConstantRestraint.h [code]
	Constant restraint.
file	core_config.h [code]
file	Cosine.h [code]
	Cosine function.
file	CoverRefined.h [code]
	Cover a bond with a sphere.
file	DataObject.h [code]
	A modifier which variables within a ball.
file	DerivativesFromRefined.h [code]
	Accumulate the derivatives of the refined particles.
file	DerivativesToRefined.h [code]
	Accumulate the derivatives of the refined particles.
file	DiameterRestraint.h [code]
	A restraint to maintain the diameter of a set of points.
file	DihedralRestraint.h [code]
	Dihedral restraint between four particles.
file	core/DistancePairScore.h [code]
	A Score on the distance between a pair of particles.
file	DistanceRestraint.h [code]
	Distance restraint between two particles.
file	DistanceToSingletonScore.h [code]
	A Score on the distance to a fixed point.
file	ExcludedVolumeRestraint.h [code]
	Prevent spheres from inter-penetrating.
file	FixedRefiner.h [code]
	A particle refiner which returns a fixed set of particles.
file	Gaussian.h [code]
	Decorator to hold Gaussian3D.
file	core/generic.h [code]
	Various important functionality for implementing decorators.
file	GridClosePairsFinder.h [code]
	Use a hierarchy of grids to find close pairs.
file	core/Harmonic.h [code]
	Harmonic function.
file	core/HarmonicLowerBound.h [code]
	Harmonic lower bound function.
file	core/HarmonicUpperBound.h [code]
	Harmonic upper bound function.
file	HarmonicWell.h [code]
	Harmonic function.
file	core/Hierarchy.h [code]
	Decorator for helping deal with a hierarchy.
file	IncrementalScoringFunction.h [code]
	Simple Monte Carlo optimizer.
file	LeavesRefiner.h [code]
	Return the hierarchy leaves under a particle.
file	Linear.h [code]
	A linear function.
file	MCCGSampler.h [code]
	A Monte Carlo/Conjugate Gradients based sampler.
file	MinimumRestraint.h [code]
	Score based on the k minimum restraints.
file	model_statistics.h [code]
	Log the restraint scores and things.
file	MonteCarlo.h [code]
	Simple Monte Carlo optimizer.
file	MonteCarloMover.h [code]
	The base class for movers for MC optimization.
file	MoveStatisticsScoreState.h [code]
	Write geometry to a file during optimization.
file	MSConnectivityRestraint.h [code]
	Mass Spec Connectivity restraint.
file	NearestNeighborsClosePairsFinder.h [code]
	Test all pairs of particles to find close pairs.
file	NeighborsTable.h [code]
	Angle restraint between three particles.
file	NormalMover.h [code]
	A modifier which perturbs a point with a normal distribution.
file	core/OpenCubicSpline.h [code]
	Open cubic spline function.
file	pair_predicates.h [code]
	Define some predicates.
file	PairConstraint.h [code]
	Use a PairModifier applied to a kernel::ParticlePairsTemp to maintain an invariant.
file	PairRestraint.h [code]
	Apply a PairScore to a Pair.
file	PeriodicOptimizerState.h [code]
	Angle restraint between three particles.
file	predicates.h [code]
	Score particles based on a bounding box.
file	core/python_only.h [code]
	Functionality only available in Python.
file	quad_predicates.h [code]
	Define some predicates.
file	QuadConstraint.h [code]
	Use a QuadModifier applied to a kernel::ParticleQuadsTemp to maintain an invariant.
file	QuadraticClosePairsFinder.h [code]
	Test all pairs of particles to find close pairs.
file	QuadRestraint.h [code]
	Apply a QuadScore to a Quad.
file	RefinedPairsPairScore.h [code]
	Generate pairs by applying a Refiner to the particles.
file	RestraintsScoringFunction.h [code]
	Storage of a model, its restraints, constraints and particles.
file	rigid_bodies.h [code]
	functionality for defining rigid bodies
file	rigid_body_geometries.h [code]
	functionality for defining rigid bodies
file	RigidBodyDistancePairScore.h [code]
	Act on the distance between two rigid bodies.
file	core/RigidBodyMover.h [code]
	A mover that transform a rigid body.
file	RigidBodyTunneler.h [code]
	A mover that transform a rigid body.
file	RigidBodyUmbrella.h [code]
	Distance restraint between two particles.
file	RigidClosePairsFinder.h [code]
	Handle rigid bodies by looking at their members.
file	SerialMover.h [code]
	A mover that applies other movers one at a time.
file	singleton_predicates.h [code]
	Define some predicates.
file	SingletonConstraint.h [code]
	Use a SingletonModifier applied to a kernel::ParticlesTemp to maintain an invariant.
file	SingletonRestraint.h [code]
	Apply a SingletonScore to a Singleton.
file	SphereDistancePairScore.h [code]
	A score on the distance between the surfaces of two spheres.
file	StatisticalPairScore.h [code]
	Functions to read mol2s.
file	SteepestDescent.h [code]
	Simple steepest descent optimizer.
file	core/symmetry.h [code]
	Implement various types of symmetry.
file	TableRefiner.h [code]
	A lookup based particle refiner.
file	Transform.h [code]
	Transform a particle.
file	TransformedDistancePairScore.h [code]
	A score on the distance between a pair of particles after transforming one.
file	triplet_predicates.h [code]
	Define some predicates.
file	TripletConstraint.h [code]
	Use a TripletModifier applied to a kernel::ParticleTripletsTemp to maintain an invariant.
file	TripletRestraint.h [code]
	Apply a TripletScore to a Triplet.
file	TruncatedHarmonic.h [code]
	Truncated harmonic.
file	Typed.h [code]
	A particle with a user-defined type.
file	TypedPairScore.h [code]
	Delegate to another PairScore depending on particle types.
file	core/utility.h [code]
	Various important functionality for implementing decorators.
file	VolumeRestraint.h [code]
	A restraint that prevents spheres from inter-penetrating.
file	WeightedDerivativesToRefined.h [code]
	Copies derivatives from coarse grained particle to its refined set of particles using weights indicated by a weight key.
file	XYZ.h [code]
	Simple XYZ decorator.
file	XYZR.h [code]
	Decorator for a sphere-like particle.