isd Directory Reference

Directory dependency graph for isd:

Files
file	AmbiguousNOERestraint.h [code]
	A lognormal restraint that uses the ISPA model to model NOE-derived distance fit.
file	AmbiguousRestraint.h [code]
	An implementation of the d-norm to make an ambiguous restraint.
file	AtomicCrossLinkMSRestraint.h [code]
	A pmf based likelihood function with prior knowledge on the false positive rate.
file	bivariate_functions.h [code]
	Classes for general functions.
file	CrossLinkData.h [code]
	Normal distribution of Function.
file	CrossLinkMSRestraint.h [code]
	A pmf based likelihood function with prior knowledge on the false positive rate.
file	CysteineCrossLinkData.h [code]
	Normal distribution of Function.
file	CysteineCrossLinkRestraint.h [code]
	A sigmoid shaped restraint between residues with discrete classifier and ambiguous assignment. To be used with cross-linking mass-spectrometry data.
file	isd/distribution.h [code]
	Base class for probability distributions.
file	em_utilities.h [code]
	Common scoring functions.
file	FNormal.h [code]
	Normal distribution of Function.
file	FretData.h [code]
	Auxiliary class useful for FRET_R restraint.
file	FretRestraint.h [code]
	FRET_R restraint to use in vivo FRET data.
file	FStudentT.h [code]
	Joint Student's t-distribution of Function.
file	GammaPrior.h [code]
	A restraint on a scale parameter.
file	GaussianAnchorEMRestraint.h [code]
	Restraint between two sets of anchor points "model" and "EM density".
file	isd/GaussianEMRestraint.h [code]
	Restrain two sets of Gaussians (model and GMM derived from EM map)
file	GaussianProcessInterpolation.h [code]
	Normal distribution of Function.
file	GaussianProcessInterpolationRestraint.h [code]
	Restraint and ScoreState for GaussianProcessInterpolation.
file	GaussianRestraint.h [code]
	A lognormal restraint that uses the ISPA model to model NOE-derived distance fit.
file	HybridMonteCarlo.h [code]
	A hybrid monte carlo implementation.
file	isd_config.h [code]
file	isd/ISDRestraint.h [code]
file	JeffreysRestraint.h [code]
	A restraint on a scale parameter.
file	LognormalAmbiguousRestraint.h [code]
	A sigmoid shaped restraint between residues with discrete classifier and ambiguous assignment. To be used with cross-linking mass-spectrometry data.
file	LognormalRestraint.h [code]
	A lognormal restraint that uses the ISPA model to model NOE-derived distance fit.
file	LogWrapper.h [code]
	Calculate the -Log of a list of restraints.
file	MarginalHBondRestraint.h [code]
	A lognormal restraint that uses the ISPA model to model HBond-derived distance fit.
file	MarginalNOERestraint.h [code]
	A lognormal restraint that uses the ISPA model to model NOE-derived distance fit.
file	isd/MolecularDynamics.h [code]
	Simple molecular dynamics optimizer.
file	MolecularDynamicsMover.h [code]
	A modifier which perturbs XYZs or Nuisances with a constant energy MD simulation.
file	MultivariateFNormalSufficient.h [code]
	Normal distribution of Function.
file	NOERestraint.h [code]
	A lognormal restraint that uses the ISPA model to model NOE-derived distance fit.
file	NormalSigmaPCRestraint.h [code]
	A Penalized Complexity prior on sigma of a normal distribution.
file	Nuisance.h [code]
	A decorator for nuisance parameters particles.
file	PenalizedComplexityPrior.h [code]
	Penalized complexity prior.
file	RepulsiveDistancePairScore.h [code]
	A simple quadric repulsive term between two atoms. Restraint is zero when the distance equals the sum of the radii plus the shift.
file	ResidueProteinProximityRestraint.h [code]
	Restrain a selection of particles (eg. a residue or segment) to be within a certain distance of a second selection of particles (eg. a protein). Use to model data from mutagenesis experiments that disrupt protein-protein interactions.
file	Scale.h [code]
	A decorator for scale parameters particles.
file	StudentTRestraint.h [code]
	A Student-t distribution restraint.
file	Switching.h [code]
	A decorator for switching parameters particles.
file	TALOSRestraint.h [code]
	TALOS dihedral restraint between four particles.
file	UniformPrior.h [code]
	A restraint on a scale parameter.
file	univariate_functions.h [code]
	Classes for general functions.
file	vonMises.h [code]
	Normal distribution of Function.
file	vonMisesKappaConjugateRestraint.h [code]
	Conjugate prior for \(\kappa\) in the von Mises distribution.
file	vonMisesKappaJeffreysRestraint.h [code]
	Jeffreys prior for \(\kappa\) in the von Mises distribution.
file	vonMisesSufficient.h [code]
	Normal distribution of Function.
file	Weight.h [code]
	Add weights constrained to the unit simplex to a particle.
file	WeightMover.h [code]
	A mover that perturbs a Weight particle.
file	WeightRestraint.h [code]
	Put description here.