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IMP Reference Guide  develop.182d9373c4,2021/04/12
The Integrative Modeling Platform
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  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.