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IMP Reference Guide
2.6.1
The Integrative Modeling Platform
IMP Manual
Reference Guide
Modules
Classes
Examples
Class List
Class Index
Class Hierarchy
Class Members
Class Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
A
CysteineCrossLinkData
(
IMP::isd
)
History
(
IMP.isd.History
)
ParticleIndexesAdaptor
(
IMP
)
SetLogTarget
(
IMP
)
CysteineCrossLinkRestraint
(
IMP::isd
)
HybridMonteCarlo
(
IMP::isd
)
ParticleIndexPairsAdaptor
(
IMP
)
SetNumberOfThreads
(
IMP
)
AddBoolFlag
(
IMP
)
D
HydrogenPDBSelector
(
IMP::atom
)
ParticleInputs
(
IMP
)
SettingsData
(
IMP::multifit
)
AddFloatFlag
(
IMP
)
I
ParticleOutputs
(
IMP
)
SetupConnectivityNetworkRestraint
(
IMP.pmi.restraints.proteomics
)
AddIntFlag
(
IMP
)
Database2
(
IMP.EMageFit.database
)
ParticlesAdaptor
(
IMP::domino
)
SetupMembraneRestraint
(
IMP.pmi.restraints.proteomics
)
AddScores
(
IMP::score_functor
)
DataObject
(
IMP::core
)
Image
(
IMP::em2d
)
ParticlesDummyRestraint
(
IMP::em2d
)
SGEPESlaveArray
(
IMP.parallel
)
AddStringFlag
(
IMP
)
DataPointsAssignment
(
IMP::multifit
)
ImageHeader
(
IMP::em
)
ParticleStates
(
IMP::domino
)
SGEQsubSlaveArray
(
IMP.parallel
)
AdvancedFlag
(
IMP
)
DecayPairContainerOptimizerState
(
IMP::misc
)
ImageReaderWriter
(
IMP::em2d
)
ParticleStatesTable
(
IMP::domino
)
Shift
(
IMP::score_functor
)
Alignment
(
IMP.pmi.analysis
)
Decorator
(
IMP
)
IMPRestraints
(
IMP.modeller
)
PartitionalClustering
(
IMP::statistics
)
Showable
(
IMP
)
AlignmentClustering
(IMP.multifit.cluster)
DefaultEmbeddingD
(
IMP::algebra
)
ImproperSingletonScore
(
IMP::atom
)
PartitionalClusteringWithCenter
(
IMP::statistics
)
SigmoidRestraintSphere
(
IMP::pmi
)
AlignSymmetric
(
IMP::cnmultifit
)
DegreesOfFreedom
(
IMP.pmi.dof
)
InBoundingBox3DSingletonPredicate
(
IMP::core
)
PathLocalPlanner
(
IMP::kinematics
)
SimpleAssignmentsTable
(
IMP::domino
)
AllBipartitePairContainer
(
IMP::container
)
DeltaDistributionFunction
(
IMP::saxs
)
InContainerPairFilter
(
IMP::container
)
PCAAligner
(
IMP::em
)
SimpleLoadLink
(
IMP::rmf
)
AllMol2Selector
(
IMP::atom
)
Demuxer
(IMP.isd.demux_trajs)
InContainerQuadFilter
(
IMP::container
)
PCAFitRestraint
(
IMP::em
)
SimpleSaveLink
(
IMP::rmf
)
AllPairContainer
(
IMP::container
)
DenseFloatLogGridKD
(
IMP::algebra
)
InContainerSingletonFilter
(
IMP::container
)
PCAFitRestraint
(
IMP::em2d
)
Simplex
(
IMP::gsl
)
AllPDBSelector
(
IMP::atom
)
DenseGrid3D
(
IMP::algebra
)
InContainerTripletFilter
(
IMP::container
)
PDBSelector
(
IMP::atom
)
Simulator
(
IMP::atom
)
AllSamePairPredicate
(
IMP::core
)
DenseGridStorageD
(
IMP::algebra
)
IncrementalScoringFunction
(
IMP::core
)
PermutationStates
(
IMP::domino
)
SingleLinkage
(
IMP::em2d
)
AllSameQuadPredicate
(
IMP::core
)
DenseIntLogGrid3D
(
IMP::algebra
)
Index
(
IMP
)
Pipe
(
IMP.isd.utils
)
SingletonConstraint
(
IMP::core
)
AllSameSingletonPredicate
(
IMP::core
)
DensityDataPoints
(
IMP::multifit
)
IndexException
(
IMP
)
PivyWriter
(
IMP::display
)
SingletonContainer
(
IMP
)
AllSameTripletPredicate
(
IMP::core
)
DensityFillingRestraint
(
IMP::em
)
IndexStates
(
IMP::domino
)
Plane3D
(
IMP::algebra
)
SingletonContainerAdaptor
(
IMP
)
AmbiguousCompositeRestraint
(
IMP.pmi.restraints.proteomics
)
DensityHeader
(
IMP::em
)
IndexVector
(
IMP
)
PlaneGeometry
(
IMP::display
)
SingletonContainerSet
(
IMP::container
)
AmbiguousNOERestraint
(
IMP::isd
)
DensityMap
(
IMP::em
)
InitialDockingFromXlinks
(
IMP.EMageFit.buildxlinks
)
Pointer
(
IMP
)
SingletonContainerStatistics
(
IMP::container
)
AmbiguousRestraint
(
IMP::isd
)
DependencyScoreState
(
IMP::domino
)
InputAdaptor
(
IMP
)
PointerMember
(
IMP
)
SingletonGeometry
(
IMP::display
)
Analysis
(IMP.isd.Analysis)
DerivativeAccumulator
(
IMP
)
InternalException
(
IMP
)
PointGeometry
(
IMP::display
)
SingletonModifier
(
IMP
)
AnalysisReplicaExchange0
(
IMP.pmi.macros
)
DerivativeCalculator
(
IMP::saxs
)
IntsOrder
(
IMP::em2d
)
PolarResamplingParameters
(
IMP::em2d
)
SingletonPredicate
(
IMP
)
AnchorsData
(
IMP::multifit
)
DerivativesFromRefined
(
IMP::core
)
IOException
(
IMP
)
PolygonGeometry
(
IMP::display
)
SingletonRestraint
(
IMP::core
)
AndPDBSelector
(
IMP::atom
)
DerivativesToRefined
(
IMP::core
)
IsCollisionPairPredicate
(
IMP::core
)
PPDBSelector
(
IMP::atom
)
SingletonsConstraint
(
IMP::container
)
Angle
(
IMP::atom
)
DiameterRestraint
(
IMP::core
)
ISDRestraint
(
IMP::isd
)
Precision
(
IMP.pmi.analysis
)
SingletonScore
(
IMP
)
AngleRestraint
(
IMP::core
)
Diffusion
(
IMP::atom
)
IsosurfaceGeometry
(
IMP::display
)
PredicatePairsRestraint
(
IMP::container
)
SingletonsGeometry
(
IMP::display
)
AngleSingletonScore
(
IMP::atom
)
Dihedral
(
IMP::atom
)
J
PredicateQuadsRestraint
(
IMP::container
)
SingletonsOptimizerState
(
IMP::container
)
AngleTripletScore
(
IMP::core
)
DihedralAngleRevoluteJoint
(
IMP::kinematics
)
PredicateSingletonScore
(
IMP::core
)
SingletonsRestraint
(
IMP::container
)
AngularVelocity
(
IMP::atom
)
DihedralRestraint
(
IMP::core
)
JeffreysRestraint
(
IMP::isd
)
PredicateSingletonsRestraint
(
IMP::container
)
SingletonStatistical
(
IMP::score_functor
)
ApplicationTestCase
(
IMP.test
)
DihedralSingletonScore
(
IMP::atom
)
Joint
(
IMP::kinematics
)
PredicateTripletsRestraint
(
IMP::container
)
SkinSurfaceGeometry
(
IMP::display
)
Array
(
IMP
)
DirectorObjectChecker
(
IMP.test
)
JPGImageReaderWriter
(
IMP::em2d
)
PrincipalComponentAnalysisD
(
IMP::algebra
)
Slave
(
IMP.parallel
)
AssemblyHeader
(
IMP::multifit
)
DiscreteSampler
(
IMP::domino
)
K
PrismaticJoint
(
IMP::kinematics
)
SlaveArray
(
IMP.parallel
)
Assignment
(
IMP::domino
)
DisjointSetsSubsetFilterTable
(
IMP::domino
)
ProbabilisticAnchorGraph
(
IMP::multifit
)
Slice
(
IMP::domino
)
AssignmentContainer
(
IMP::domino
)
DistanceFilter
(
IMP::em2d
)
KClosePairsPairScore
(
IMP::core
)
ProbabilisticSubsetFilterTable
(
IMP::domino
)
SmoothingFunction
(
IMP::atom
)
AssignmentsTable
(
IMP::domino
)
DistanceFilterTable
(
IMP::em2d
)
KernelParameters
(
IMP::em
)
ProcessOutput
(
IMP.pmi.output
)
Soap
(
IMP::score_functor
)
Atom
(
IMP::atom
)
DistanceMask
(
IMP::em
)
Key
(
IMP
)
Profile
(
IMP::saxs
)
SoapPairFilter
(
IMP::atom
)
AtomicCrossLinkMSRestraint
(
IMP.pmi.restraints.crosslinking
)
DistancePairScore
(
IMP::core
)
KinematicForest
(
IMP::kinematics
)
ProfileClustering
(
IMP::saxs
)
SoftCylinderPairScore
(
IMP::misc
)
AtomicCrossLinkMSRestraint
(
IMP::isd
)
DistancePairScore
(
IMP::score_functor
)
KinematicForestScoreState
(
IMP::kinematics
)
ProfileFitter
(
IMP::saxs
)
SoftSpherePairScore
(
IMP::core
)
ATOMPDBSelector
(
IMP::atom
)
DistanceRestraint
(
IMP.pmi.restraints.basic
)
KinematicNode
(
IMP::kinematics
)
Profiler
(
IMP::benchmark
)
SolventAccessibleSurface
(
IMP::saxs
)
AtomType
(
IMP::atom
)
DistanceRestraint
(
IMP::core
)
KMeans
(
IMP::kmeans
)
ProjectingOptions
(
IMP::em2d
)
SparseGrid3D
(
IMP::algebra
)
AtomTypePDBSelector
(
IMP::atom
)
DistributePairsScoreState
(
IMP::container
)
L
ProjectingParameters
(
IMP::em2d
)
SparseGridStorageD
(
IMP::algebra
)
AttributeOptimizer
(
IMP
)
DistributeQuadsScoreState
(
IMP::container
)
ProjectionFinder
(
IMP::em2d
)
SparseSymmetricPairMemoizer
(
IMP
)
AttributeSingletonPredicate
(
IMP::core
)
DistributeSingletonsScoreState
(
IMP::container
)
LabelGeometry
(
IMP::display
)
ProjectionMask
(
IMP::em2d
)
SparseUnboundedGrid3D
(
IMP::algebra
)
AverageDistanceLinkage
(
IMP::em2d
)
DistributeTripletsScoreState
(
IMP::container
)
LangevinThermostatOptimizerState
(
IMP::atom
)
ProjectionParameters
(
IMP::em2d
)
SparseUnboundedGridD
(
IMP::algebra
)
B
Distribution
(
IMP::saxs
)
LeavesRefiner
(
IMP::core
)
ProjectionParametersScoreState
(
IMP::em2d
)
SphereD
(
IMP::algebra
)
DockOrder
(
IMP.EMageFit.buildxlinks
)
LennardJones
(
IMP::atom
)
ProjectionStates
(
IMP::em2d
)
SphereDistance
(
IMP::score_functor
)
BackbonePDBSelector
(
IMP::atom
)
DOF
(
IMP::kinematics
)
LennardJonesPairScore
(
IMP::atom
)
ProteinKinematics
(
IMP::kinematics
)
SphereDistancePairScore
(
IMP::core
)
BallMover
(
IMP::core
)
DOFsSampler
(
IMP::kinematics
)
LessPairBySecond
(
IMP::em2d
)
ProteinLigandAtomPairScore
(
IMP::atom
)
SphereDistanceToSingletonScore
(
IMP::core
)
BallMover
(
IMP::symmetry
)
Domain
(
IMP::atom
)
Linear
(
IMP::core
)
ProteinLigandRestraint
(
IMP::atom
)
SphereGeometry
(
IMP::display
)
BerendsenThermostatOptimizerState
(
IMP::atom
)
DominoModel
(
IMP.EMageFit.domino_model
)
Linear1DFunction
(
IMP::isd
)
ProteinsAnchorsSamplingSpace
(
IMP::multifit
)
SpherePatch3D
(
IMP::algebra
)
BinormalTerm
(
IMP::modeller
)
DominoSampler
(
IMP::domino
)
LinearFit2D
(
IMP::algebra
)
ProteomicsData
(
IMP::multifit
)
SphericalVector3D
(
IMP::algebra
)
BiStableDistanceRestraint
(
IMP.pmi.restraints.basic
)
Dope
(
IMP::score_functor
)
LinearLowerBound
(
IMP::score_functor
)
ProteomicsEMAlignmentAtomic
(
IMP::multifit
)
SpiderHeader
(
IMP::em
)
BivariateFunction
(
IMP::isd
)
DopePairScore
(
IMP::atom
)
LinearVelocity
(
IMP::atom
)
PseudoAtomicRestraint
(
IMP.pmi.restraints.stereochemistry
)
SpiderImageReaderWriter
(
IMP::em2d
)
Bond
(
IMP::atom
)
DummyRestraint
(
IMP::em2d
)
ListAssignmentContainer
(
IMP::domino
)
PymolWriter
(
IMP::display
)
SpiderMapReaderWriter
(
IMP::em
)
ForceFieldParameters::Bond
(
IMP::atom
)
DummyRestraint
(
IMP::multifit
)
ListAssignmentsTable
(
IMP::domino
)
PythonDirectedGraph
(
IMP
)
State
(
IMP.pmi.topology
)
BondAngleRevoluteJoint
(
IMP::kinematics
)
DynamicListPairContainer
(
IMP::container
)
ListPairContainer
(
IMP::container
)
PythonExampleConstraint
(
IMP.example
)
State
(
IMP::atom
)
Bonded
(
IMP::atom
)
DynamicListQuadContainer
(
IMP::container
)
ListQuadContainer
(
IMP::container
)
PythonExamplePairScore
(
IMP.example
)
StateAdaptor
(
IMP::misc
)
BondedPairFilter
(
IMP::atom
)
DynamicListSingletonContainer
(
IMP::container
)
ListSingletonContainer
(
IMP::container
)
PythonExampleRestraint
(
IMP.example
)
Statistical
(
IMP::score_functor
)
BondEndpointsRefiner
(
IMP::atom
)
DynamicListTripletContainer
(
IMP::container
)
ListSubsetFilterTable
(
IMP::domino
)
PythonExampleSingletonModifier
(
IMP.example
)
StatisticalPairScore
(
IMP::core
)
BondGeometry
(
IMP::atom
)
DynamicNearestNeighbor3D
(
IMP::algebra
)
ListTripletContainer
(
IMP::container
)
PythonExampleUnaryFunction
(
IMP.example
)
Statistics
(IMP.isd.Statistics)
BondGraph
(
IMP::atom
)
E
LoadLink
(
IMP::rmf
)
Q
SteepestDescent
(
IMP::core
)
BondPairContainer
(
IMP::atom
)
LocalPlanner
(
IMP::kinematics
)
StereochemistryPairFilter
(
IMP::atom
)
BondsGeometry
(
IMP::atom
)
EdgePairGeometry
(
IMP::core
)
LocalSlave
(
IMP.parallel
)
QuadConstraint
(
IMP::core
)
StructureSource
(
IMP::atom
)
BondSingletonScore
(
IMP::atom
)
EdgePairsGeometry
(
IMP::core
)
LogEmbeddingD
(
IMP::algebra
)
QuadContainer
(
IMP
)
Subset
(
IMP::domino
)
BoundedGridRangeD
(
IMP::algebra
)
ElasticNetworkRestraint
(
IMP.pmi.restraints.stereochemistry
)
LogHolder
(IMP.isd.demux_trajs)
QuadContainerAdaptor
(
IMP
)
SubsetFilter
(
IMP::domino
)
BoundingBoxD
(
IMP::algebra
)
ElectronMicroscopy2D
(
IMP.pmi.restraints.em2d
)
LognormalAmbiguousRestraint
(
IMP::isd
)
QuadContainerSet
(
IMP::container
)
SubsetFilterTable
(
IMP::domino
)
BoundingBoxGeometry
(
IMP::display
)
ElectronMicroscopy2D_FFT
(
IMP.pmi.restraints.em2d
)
LognormalRestraint
(
IMP::isd
)
QuadContainerStatistics
(
IMP::container
)
SurfaceMeshGeometry
(
IMP::display
)
BoxSweepClosePairsFinder
(
IMP::core
)
ElementTable
(
IMP::atom
)
LogPairScore
(
IMP::misc
)
QuadModifier
(
IMP
)
SurfaceShellDensityMap
(
IMP::em
)
BranchAndBoundAssignmentsTable
(
IMP::domino
)
Ellipsoid3D
(
IMP::algebra
)
LogWrapper
(
IMP::isd
)
QuadPredicate
(
IMP
)
Switching
(
IMP::isd
)
BranchAndBoundSampler
(
IMP::domino
)
EllipsoidGeometry
(
IMP::display
)
LowestRefinedPairScore
(
IMP::misc
)
QuadraticClosePairsFinder
(
IMP::core
)
Symmetric
(
IMP::pmi
)
BrownianDynamics
(
IMP::atom
)
Em2DRestraint
(
IMP::em2d
)
LRUCache
(
IMP
)
QuadRestraint
(
IMP::core
)
SymmetryRestraint
(
IMP.pmi.restraints.stereochemistry
)
BrownianDynamicsTAMD
(
IMP::atom
)
Em2DRestraintParameters
(
IMP::em2d
)
M
QuadsConstraint
(
IMP::container
)
System
(
IMP.pmi.topology
)
BuildModel
(
IMP.pmi.macros
)
EM2DScore
(
IMP::em2d
)
QuadScore
(
IMP
)
T
BuildModel1
(
IMP.pmi.macros
)
Embedding
(
IMP::statistics
)
Manager
(
IMP.parallel
)
QuadsOptimizerState
(
IMP::container
)
BuildSystem
(
IMP.pmi.macros
)
EMReaderWriter
(
IMP::em
)
MapDistanceTransform
(
IMP::em
)
QuadsRestraint
(
IMP::container
)
TableRefiner
(
IMP::core
)
C
Ensemble
(
IMP::multifit
)
MapReaderWriter
(
IMP::em
)
QuasiNewton
(
IMP::gsl
)
TALOSReader
(
IMP.isd.TALOSReader
)
EnsembleGenerator
(
IMP::multi_state
)
MarginalHBondRestraint
(
IMP::isd
)
R
TALOSRestraint
(
IMP::isd
)
CAAngleRestraint
(
IMP::atom
)
Entry
(
IMP.isd.Entry
)
MarginalNOERestraint
(
IMP::isd
)
TAMDCentroid
(
IMP::atom
)
CADihedralRestraint
(
IMP::atom
)
EnvelopeFitRestraint
(
IMP::em
)
MasksManager
(
IMP::em2d
)
RadialDistributionFunction
(
IMP::saxs
)
TAMDParticle
(
IMP::atom
)
CAlphaPDBSelector
(
IMP::atom
)
EnvelopePenetrationRestraint
(
IMP::em
)
Mass
(
IMP::atom
)
RadiusDependentDistanceMask
(
IMP::em
)
TempDir
(
IMP.test
)
CappedAssignmentContainer
(
IMP::domino
)
EnvelopeScore
(
IMP::em
)
MasterCommunicator
(
IMP.parallel.master_communicator
)
RadiusOfGyrationRestraint
(
IMP::saxs
)
TempResidue
(
IMP.pmi.topology
)
CBetaPDBSelector
(
IMP::atom
)
EqualitySubsetFilterTable
(
IMP::domino
)
MatchTemplateResult
(
IMP::em2d
)
RadiusOfGyrationRestraint
(
IMP::multifit
)
TestCase
(
IMP.test
)
CCDLoopClosure
(
IMP::kinematics
)
EquivalenceAndExclusionSubsetFilterTable
(
IMP::domino
)
MaxVectorKDMetric
(
IMP::algebra
)
RAII
(
IMP
)
TextInput
(
IMP
)
CenteredMat
(
IMP::em2d
)
EquivalenceSubsetFilterTable
(
IMP::domino
)
MCCGSampler
(
IMP::core
)
RangeViewAssignmentContainer
(
IMP::domino
)
TextOutput
(
IMP
)
CenterOfMass
(
IMP::atom
)
Error
(
IMP.parallel
)
MeanAbsoluteDifference
(
IMP::em2d
)
RatioVolatilityScore
(
IMP::saxs
)
TextWriter
(
IMP::display
)
Centroid
(
IMP::core
)
EuclideanMetric
(
IMP::statistics
)
MembraneRestraint
(
IMP::pmi
)
ReadAssignmentContainer
(
IMP::domino
)
TIFFImageReaderWriter
(
IMP::em2d
)
CentroidOfRefined
(
IMP::core
)
EuclideanVectorKDMetric
(
IMP::algebra
)
Memoizer
(
IMP
)
ReadHDF5AssignmentContainer
(
IMP::domino
)
Timer
(
IMP
)
Chain
(
IMP::atom
)
EvaluationState
(
IMP
)
MergeTreeBuilder
(
IMP::multifit
)
RecursiveAssignmentsTable
(
IMP::domino
)
TopologyPlot
(IMP.pmi.plotting.topology)
ChainPDBSelector
(
IMP::atom
)
EventException
(
IMP
)
Metric
(
IMP::statistics
)
RecursivePartitionalClusteringEmbedding
(
IMP::statistics
)
TopologyReader
(
IMP.pmi.topology
)
Charged
(
IMP::atom
)
EventPairsOptimizerState
(
IMP::container
)
MetricClosePairsFinder
(
IMP::misc
)
RecursivePartitionalClusteringMetric
(
IMP::statistics
)
TotalScoreOutput
(
IMP.pmi.io
)
CHARMMAtom
(
IMP::atom
)
EventQuadsOptimizerState
(
IMP::container
)
MinimumPairRestraint
(
IMP::container
)
RecursiveStates
(
IMP::domino
)
Transform
(
IMP::core
)
CHARMMAtomTopology
(
IMP::atom
)
EventSingletonsOptimizerState
(
IMP::container
)
MinimumPairScore
(
IMP::container
)
RefCountChecker
(
IMP.test
)
Transformation2D
(
IMP::algebra
)
CHARMMBondEndpoint
(
IMP::atom
)
EventTripletsOptimizerState
(
IMP::container
)
MinimumQuadRestraint
(
IMP::container
)
Reference
(
IMP::core
)
Transformation3D
(
IMP::algebra
)
CHARMMBondParameters
(
IMP::atom
)
ExampleComplexRestraint
(
IMP::example
)
MinimumQuadScore
(
IMP::container
)
ReferenceFrame3D
(
IMP::algebra
)
Transformation3DToText
(
IMP.EMageFit.imp_general.io
)
CHARMMConnection
(
IMP::atom
)
ExampleConstraint
(
IMP::example
)
MinimumRestraint
(
IMP::core
)
ReferenceFrameGeometry
(
IMP::display
)
TransformationAndReflectionSymmetry
(
IMP::core
)
CHARMMDihedralParameters
(
IMP::atom
)
ExampleDecorator
(
IMP::example
)
MinimumRestraintScoreSubsetFilterTable
(
IMP::domino
)
ReferenceFrameToText
(
IMP.EMageFit.imp_general.io
)
TransformationJoint
(
IMP::kinematics
)
CharmmForceFieldRestraint
(
IMP.pmi.restraints.stereochemistry
)
ExampleObject
(
IMP::example
)
MinimumSingletonRestraint
(
IMP::container
)
RefinedPairsPairScore
(
IMP::core
)
TransformationSymmetry
(
IMP::core
)
CHARMMIdealResidueTopology
(
IMP::atom
)
ExamplePairScore
(
IMP::example
)
MinimumSingletonScore
(
IMP::container
)
Refiner
(
IMP
)
TransformationSymmetryMover
(
IMP::core
)
CHARMMInternalCoordinate
(
IMP::atom
)
ExampleRestraint
(
IMP::example
)
MinimumTripletRestraint
(
IMP::container
)
Reflection3D
(
IMP::algebra
)
TransformedDistancePairScore
(
IMP::core
)
CHARMMParameters
(
IMP::atom
)
ExampleSingletonModifier
(
IMP::example
)
MinimumTripletScore
(
IMP::container
)
RegistrationResult
(
IMP::em2d
)
TransformMover
(
IMP::pmi
)
CHARMMPatch
(
IMP::atom
)
ExampleSubsetFilterTable
(
IMP::example
)
Model
(
IMP
)
RelativePositionMover
(
IMP::em2d
)
Triangle3D
(
IMP::algebra
)
CHARMMResidueTopology
(
IMP::atom
)
ExampleTemplateClassD
(
IMP::example
)
ModelException
(
IMP
)
RemoteError
(
IMP.parallel
)
TriangleGeometry
(
IMP::display
)
CHARMMResidueTopologyBase
(
IMP::atom
)
ExampleUnaryFunction
(
IMP::example
)
ModellerRestraints
(
IMP.modeller
)
RemoveRigidMotionOptimizerState
(
IMP::atom
)
TripletConstraint
(
IMP::core
)
CHARMMSegmentTopology
(
IMP::atom
)
Exception
(
IMP
)
ModelLoader
(
IMP.modeller
)
RemoveTranslationOptimizerState
(
IMP::atom
)
TripletContainer
(
IMP
)
CHARMMStereochemistryRestraint
(
IMP::atom
)
ExcludedVolumeRestraint
(
IMP::core
)
ModelObject
(
IMP
)
ReplicaExchange
(
IMP.pmi.samplers
)
TripletContainerAdaptor
(
IMP
)
CHARMMTopology
(
IMP::atom
)
ExcludedVolumeSphere
(
IMP.pmi.restraints.stereochemistry
)
ModifierVisitor
(
IMP::core
)
ReplicaExchange
(
IMP::mpi
)
TripletContainerSet
(
IMP::container
)
ChecksScoreState
(
IMP::core
)
ExclusionSubsetFilterTable
(
IMP::domino
)
Mol2Selector
(
IMP::atom
)
ReplicaExchange0
(
IMP.pmi.macros
)
TripletContainerStatistics
(
IMP::container
)
ChiFreeScore
(
IMP::saxs
)
ExclusiveConsecutivePairContainer
(
IMP::container
)
MolCnSymmAxisDetector
(
IMP::cnmultifit
)
Representation
(
IMP::atom
)
TripletModifier
(
IMP
)
ChildrenRefiner
(
IMP::core
)
ExclusiveConsecutivePairFilter
(
IMP::container
)
MolecularDynamics
(
IMP::atom
)
Representation
(
IMP.pmi.representation
)
TripletPredicate
(
IMP
)
ChiScore
(
IMP::saxs
)
ExtendedGridIndexD
(
IMP::algebra
)
MolecularDynamics
(
IMP.pmi.samplers
)
RepulsiveDistancePairScore
(
IMP::isd
)
TripletRestraint
(
IMP::core
)
ChiScoreLog
(
IMP::saxs
)
EzRestraint
(
IMP::atom
)
MolecularDynamics
(
IMP::isd
)
Residue
(
IMP::atom
)
TripletsConstraint
(
IMP::container
)
ChiSquaredScore
(
IMP::em2d
)
F
MolecularDynamicsMover
(
IMP::isd
)
ResidueAngleRestraint
(
IMP.pmi.restraints.stereochemistry
)
TripletScore
(
IMP
)
ChiSquareMetric
(
IMP::statistics
)
Molecule
(
IMP::atom
)
ResidueBondRestraint
(
IMP.pmi.restraints.stereochemistry
)
TripletsOptimizerState
(
IMP::container
)
CloseBipartitePairContainer
(
IMP::container
)
FFTFitting
(
IMP::multifit
)
Molecule
(
IMP.pmi.topology
)
ResidueDihedralRestraint
(
IMP.pmi.restraints.stereochemistry
)
TripletsRestraint
(
IMP::container
)
ClosedCubicSpline
(
IMP::core
)
FFTFittingOutput
(
IMP::multifit
)
MonteCarlo
(
IMP.pmi.samplers
)
ResiduePairListParser
(
IMP.pmi.io.crosslink
)
TruncatedHarmonic
(
IMP::core
)
ClosePairContainer
(
IMP::container
)
FilterGeometry
(
IMP::display
)
MonteCarlo
(
IMP::core
)
ResidueRotamer
(
IMP::rotamer
)
Typed
(
IMP::core
)
ClosePairsFinder
(
IMP::core
)
FilterOperator
(
IMP.pmi.io.crosslink
)
MonteCarloMover
(
IMP::core
)
ResidueType
(
IMP::atom
)
TypedPairScore
(
IMP::core
)
ClosePairsPairScore
(
IMP::core
)
Fine2DRegistrationRestraint
(
IMP::em2d
)
MonteCarloMoverResult
(
IMP::core
)
ResidueTypePDBSelector
(
IMP::atom
)
TypeException
(
IMP
)
Clustering
(
IMP.pmi.analysis
)
FitParameters
(
IMP::saxs
)
MonteCarloRelativeMoves
(
IMP.EMageFit.monte_carlo
)
Resolution
(
IMP::pmi
)
U
ClusterSet
(
IMP::em2d
)
FitRestraint
(
IMP::em
)
MonteCarloWithBasinHopping
(
IMP::core
)
Restraint
(
IMP::saxs
)
CnSymmAxisDetector
(
IMP::cnmultifit
)
FittingSolutionRecord
(
IMP::multifit
)
MonteCarloWithLocalOptimization
(
IMP::core
)
Restraint
(
IMP
)
UnaryFunction
(
IMP
)
CoarseCC
(
IMP::em
)
FittingSolutions
(
IMP::em
)
MoveStatisticsScoreState
(
IMP::core
)
RestraintCache
(
IMP::domino
)
UnaryFunctionEvaluate
(
IMP::score_functor
)
CoarseCCatIntervals
(
IMP::em
)
FittingStates
(
IMP::multifit
)
MRCReaderWriter
(
IMP::em
)
RestraintGeometry
(
IMP::display
)
UnboundedGridRangeD
(
IMP::algebra
)
CoarseConvolution
(
IMP::em
)
FixedFormatParser
(
IMP.pmi.io.crosslink
)
MSConnectivityRestraint
(
IMP::core
)
RestraintsAdaptor
(
IMP
)
Uncertainty
(
IMP::pmi
)
CoinFlipPairPredicate
(
IMP::core
)
FixedRefiner
(
IMP::core
)
MultipleBinormalRestraint
(
IMP::modeller
)
RestraintScoreSubsetFilterTable
(
IMP::domino
)
UncheckedWeakPointer
(
IMP
)
CoinFlipQuadPredicate
(
IMP::core
)
FixedXYZ
(
IMP::algebra
)
MultiStateModel
(
IMP::multi_state
)
RestraintSet
(
IMP
)
Undecorator
(
IMP
)
CoinFlipSingletonPredicate
(
IMP::core
)
Flag
(
IMP
)
MultiStateModelScore
(
IMP::multi_state
)
RestraintSetGeometry
(
IMP::display
)
UniformBackboneSampler
(
IMP::kinematics
)
CoinFlipTripletPredicate
(
IMP::core
)
FloatIndex
(
IMP
)
MultivariateFNormalSufficient
(
IMP::isd
)
RestraintsScoringFunction
(
IMP::core
)
UniformPrior
(
IMP::isd
)
CollisionCrossSection
(
IMP::em2d
)
FNormal
(
IMP::isd
)
MyMetric
(write_a_metric)
ResultsDB
(
IMP.EMageFit.solutions_io
)
UnivariateFunction
(
IMP::isd
)
Color
(
IMP::display
)
ForceFieldParameters
(
IMP::atom
)
N
RevoluteJoint
(
IMP::kinematics
)
UnorderedTypePairPredicate
(
IMP::core
)
ColorChange
(
IMP.pmi.tools
)
ForceSwitch
(
IMP::atom
)
RevoluteJointMover
(
IMP::kinematics
)
UnorderedTypeQuadPredicate
(
IMP::core
)
Colored
(
IMP::display
)
FormFactorTable
(
IMP::saxs
)
NearestNeighborD
(
IMP::algebra
)
RigidBodiesImageFitRestraint
(
IMP::em2d
)
UnorderedTypeSingletonPredicate
(
IMP::core
)
CommandDispatcher
(
IMP
)
Fragment
(
IMP::atom
)
NearestNeighborsClosePairsFinder
(
IMP::core
)
RigidBodiesProfileHandler
(
IMP::saxs
)
UnorderedTypeTripletPredicate
(
IMP::core
)
CommonEndpointPairFilter
(
IMP::misc
)
FretData
(
IMP::isd
)
NeighborsTable
(
IMP::core
)
RigidBody
(
IMP::core
)
UsageException
(
IMP
)
CompareMultiStateModels
(
IMP::multi_state
)
FretRestraint
(
IMP::isd
)
NestedRigidBodyStates
(
IMP::domino
)
RigidBodyAnglePairScore
(
IMP::core
)
V
ComplementarityRestraint
(
IMP::multifit
)
FuzzyBoolean
(
IMP.pmi.restraints.proteomics
)
NetworkError
(
IMP.parallel
)
RigidBodyDerivativeGeometry
(
IMP::core
)
CompleteLinkage
(
IMP::em2d
)
FuzzyRestraint
(
IMP.pmi.restraints.proteomics
)
NOERestraint
(
IMP::isd
)
RigidBodyDerivativesGeometry
(
IMP::core
)
Value
(
IMP
)
ComponentHeader
(
IMP::multifit
)
G
NoMoreSlavesError
(
IMP.parallel
)
RigidBodyDiffusion
(
IMP::atom
)
ValueException
(
IMP
)
ComponentTopology
(
IMP.pmi.topology
)
NonAlternativePDBSelector
(
IMP::atom
)
RigidBodyDistancePairScore
(
IMP::core
)
Vector
(
IMP
)
CompositeJoint
(
IMP::kinematics
)
Gaussian
(
IMP::core
)
NonCopyable
(
IMP
)
RigidBodyFrameGeometry
(
IMP::core
)
VectorBaseD
(
IMP::algebra
)
CompositeRestraint
(
IMP.pmi.restraints.proteomics
)
Gaussian3D
(
IMP::algebra
)
NonHydrogenMol2Selector
(
IMP::atom
)
RigidBodyFramesGeometry
(
IMP::core
)
VectorD
(
IMP::algebra
)
CompositeRestraint
(
IMP::pmi
)
GaussianEMRestraint
(
IMP.pmi.restraints.em
)
NonRigidMember
(
IMP::core
)
RigidBodyHierarchyGeometry
(
IMP::core
)
VectorDEmbedding
(
IMP::statistics
)
CompoundStates
(
IMP::domino
)
GaussianEMRestraint
(
IMP::isd
)
NonWaterNonHydrogenPDBSelector
(
IMP::atom
)
RigidBodyMember
(
IMP::core
)
VectorKDMetric
(
IMP::algebra
)
Cone3D
(
IMP::algebra
)
GaussianProcessInterpolation
(
IMP::isd
)
NonWaterPDBSelector
(
IMP::atom
)
RigidBodyMover
(
IMP::core
)
VelocityScalingOptimizerState
(
IMP::atom
)
Configuration
(
IMP
)
GaussianProcessInterpolationRestraint
(
IMP::isd
)
NormalizedSphereDistancePairScore
(
IMP::core
)
RigidBodyMover
(
IMP::symmetry
)
VersionInfo
(
IMP
)
ConfigurationSet
(
IMP
)
GaussianRestraint
(
IMP::isd
)
NormalMover
(
IMP::core
)
RigidBodyStates
(
IMP::domino
)
VolumeRestraint
(
IMP::core
)
ConfigurationSetRMSDMetric
(
IMP::statistics
)
GeneralizedGuinierPorodFunction
(
IMP::isd
)
NotPDBSelector
(
IMP::atom
)
RigidBodyTorque
(
IMP::core
)
Voxel
(
IMP::em
)
ConfigurationSetXYZEmbedding
(
IMP::statistics
)
GenericAttributeSingletonScore
(
IMP::core
)
NPDBSelector
(
IMP::atom
)
RigidBodyTunneler
(
IMP::core
)
W
ConjugateGradients
(
IMP.pmi.samplers
)
GenericBoundingBox3DSingletonScore
(
IMP::core
)
Nuisance
(
IMP::isd
)
RigidBodyUmbrella
(
IMP::core
)
ConjugateGradients
(
IMP::gsl
)
GenericDistanceToSingletonScore
(
IMP::core
)
O
RigidClosePairsFinder
(
IMP::core
)
WarningContext
(
IMP
)
ConjugateGradients
(
IMP::core
)
GeometricHash
(
IMP::multifit
)
RigidMember
(
IMP::core
)
WaterPDBSelector
(
IMP::atom
)
ConnectingPairContainer
(
IMP::container
)
GeometricPrimitiveD
(
IMP::algebra
)
Object
(
IMP
)
RMSDOutput
(
IMP.pmi.io
)
WeakPointer
(
IMP
)
ConnectivityCrossLinkMS
(
IMP.pmi.restraints.crosslinking
)
Geometry
(
IMP::display
)
OpenCubicSpline
(
IMP::core
)
RotamerAngleTuple
(
IMP::rotamer
)
Weight
(
IMP::isd
)
ConnectivityNetworkRestraint
(
IMP.pmi.restraints.proteomics
)
GeometryProcessor
(
IMP::display
)
OpenCubicSpline
(
IMP::score_functor
)
RotamerCalculator
(
IMP::rotamer
)
WeightedDerivativesToRefined
(
IMP::core
)
ConnectivityRestraint
(
IMP.pmi.restraints.proteomics
)
GeometrySet
(
IMP::display
)
Optimizer
(
IMP
)
RotamerLibrary
(
IMP::rotamer
)
WeightedExcludedVolumeRestraint
(
IMP::multifit
)
ConnectivityRestraint
(
IMP.pmi.restraints.stereochemistry
)
GetModelDensity
(
IMP.pmi.analysis
)
OptimizerState
(
IMP
)
Rotation2D
(
IMP::algebra
)
WeightedFitParameters
(
IMP::saxs
)
ConnectivityRestraint
(
IMP::core
)
GridClosePairsFinder
(
IMP::core
)
OptionParser
(
IMP
)
Rotation3D
(
IMP::algebra
)
WeightedProfileFitter
(
IMP::saxs
)
ConnollySurfacePoint
(
IMP::algebra
)
GridD
(
IMP::algebra
)
Order
(
IMP::domino
)
RRT
(
IMP::kinematics
)
WeightedSphereDistancePairScore
(
IMP::core
)
ConsecutivePairContainer
(
IMP::container
)
GridIndexD
(
IMP::algebra
)
OrderedDefaultDict
(
IMP.pmi.tools
)
RunInTempDir
(
IMP.test
)
WeightMover
(
IMP::isd
)
ConsecutivePairFilter
(
IMP::container
)
GridStates
(
IMP::em2d
)
OrderedTypePairPredicate
(
IMP::core
)
S
WeightRestraint
(
IMP::isd
)
ConstantPairPredicate
(
IMP::core
)
GSLOptimizer
(
IMP::gsl
)
OrderedTypeQuadPredicate
(
IMP::core
)
WeightScore
(
IMP::score_functor
)
ConstantQuadPredicate
(
IMP::core
)
H
OrderedTypeSingletonPredicate
(
IMP::core
)
SameResiduePairFilter
(
IMP::atom
)
WormLikeChain
(
IMP::misc
)
ConstantRestraint
(
IMP::core
)
OrderedTypeTripletPredicate
(
IMP::core
)
SampleAssignmentContainer
(
IMP::domino
)
WriteAssignmentContainer
(
IMP::domino
)
ConstantSingletonPredicate
(
IMP::core
)
Harmonic
(
IMP::core
)
OrientedSoap
(
IMP::score_functor
)
SampledDensityMap
(
IMP::em
)
WriteHDF5AssignmentContainer
(
IMP::domino
)
ConstantTripletPredicate
(
IMP::core
)
Harmonic
(
IMP::score_functor
)
OrientedSoapPairScore
(
IMP::atom
)
Sampler
(
IMP
)
WriteOptimizerState
(
IMP::display
)
Constraint
(
IMP
)
HarmonicDistancePairScore
(
IMP::core
)
OrPDBSelector
(
IMP::atom
)
SaveLink
(
IMP::rmf
)
WritePDBOptimizerState
(
IMP::atom
)
ConstVector
(
IMP
)
HarmonicLowerBound
(
IMP::core
)
Output
(
IMP.pmi.output
)
SaveOptimizerState
(
IMP::rmf
)
Writer
(
IMP::display
)
Container
(
IMP
)
HarmonicLowerBound
(
IMP::score_functor
)
P
SaveToConfigurationSetOptimizerState
(
IMP
)
WriterAdaptor
(
IMP::display
)
Context
(
IMP.parallel
)
HarmonicSphereDistancePairScore
(
IMP::core
)
SAXSMultiStateModelScore
(
IMP::multi_state
)
WriteRestraintScoresOptimizerState
(
IMP::core
)
Copy
(
IMP::atom
)
HarmonicUpperBound
(
IMP::core
)
PackedAssignmentContainer
(
IMP::domino
)
Scale
(
IMP::isd
)
X
Cosine
(
IMP::core
)
HarmonicUpperBound
(
IMP::score_functor
)
PairConstraint
(
IMP::core
)
ScopedAddCacheAttribute
(
IMP
)
CoulombPairScore
(
IMP::atom
)
HarmonicUpperBoundSphereDiameterPairScore
(
IMP::core
)
PairContainer
(
IMP
)
ScopedSetAttribute
(
IMP
)
Xlink
(
IMP.EMageFit.buildxlinks
)
Covariance1DFunction
(
IMP::isd
)
HarmonicUpperBoundSphereDistancePairScore
(
IMP::core
)
PairContainerAdaptor
(
IMP
)
Score
(
IMP::score_functor
)
XlinksDict
(
IMP.EMageFit.buildxlinks
)
Cover
(
IMP::core
)
HarmonicWell
(
IMP::core
)
PairContainerSet
(
IMP::container
)
ScoreAccumulator
(
IMP
)
XLTable
(
IMP.pmi.io.xltable
)
CoverBond
(
IMP::atom
)
HasHigherCCC
(
IMP::em2d
)
PairContainerStatistics
(
IMP::container
)
ScoreFunction
(
IMP::em2d
)
XorPDBSelector
(
IMP::atom
)
CoverRefined
(
IMP::core
)
HasLowerScore
(
IMP::em2d
)
PairGeometry
(
IMP::display
)
ScoreState
(
IMP
)
XplorReaderWriter
(
IMP::em
)
CPDBSelector
(
IMP::atom
)
HeapAssignmentContainer
(
IMP::domino
)
PairListSubsetFilterTable
(
IMP::domino
)
ScoreUnaryFunction
(
IMP::score_functor
)
XYZ
(
IMP::core
)
CreateLogContext
(
IMP
)
HeapRecord
(
IMP.EMageFit.solutions_io
)
PairModifier
(
IMP
)
ScoringFunction
(
IMP
)
XYZDerivativeGeometry
(
IMP::core
)
CrossCorrelationRestraint
(
IMP.pmi.restraints.em
)
HierarchiesGeometry
(
IMP::atom
)
PairPredicate
(
IMP
)
ScoringFunctionAdaptor
(
IMP
)
XYZDerivativesGeometry
(
IMP::core
)
CrossLinkData
(
IMP::isd
)
Hierarchy
(
IMP::core
)
PairRestraint
(
IMP::core
)
SecondaryStructure
(
IMP.pmi.restraints.stereochemistry
)
XYZR
(
IMP::core
)
CrossLinkDataBaseFromStructure
(
IMP.pmi.io.crosslink
)
Hierarchy
(
IMP::atom
)
PairsConstraint
(
IMP::container
)
SecondaryStructureResidue
(
IMP::atom
)
XYZRGeometry
(
IMP::core
)
CrossLinkDataBaseKeywordsConverter
(
IMP.pmi.io.crosslink
)
HierarchyCounter
(
IMP::core
)
PairScore
(
IMP
)
Segment3D
(
IMP::algebra
)
XYZRsGeometry
(
IMP::core
)
CrossLinkingMassSpectrometryRestraint
(
IMP.pmi.restraints.crosslinking
)
HierarchyDatabase
(
IMP.pmi.tools
)
PairsGeometry
(
IMP::display
)
SegmentationParameters
(
IMP::em2d
)
XYZStates
(
IMP::domino
)
CrossLinkMS
(IMP.pmi.nonmantained)
HierarchyGeometry
(
IMP::atom
)
PairsOptimizerState
(
IMP::container
)
SegmentGeometry
(
IMP::display
)
p
CrossLinkMSRestraint
(
IMP::isd
)
HierarchyLoadLink
(
IMP::rmf
)
PairsRestraint
(
IMP::container
)
Selection
(
IMP::atom
)
CrossLinkTable
(
IMP.pmi.analysis
)
HierarchySaveLink
(
IMP::rmf
)
ParabolicFit2D
(
IMP::algebra
)
SelectionGeometry
(
IMP::atom
)
piecewise_linear_distribution
(
IMP
)
CustomXYZR
(
IMP::misc
)
HierarchyTraits
(
IMP::core
)
Particle
(
IMP
)
Sequences
(
IMP.pmi.topology
)
s
CvEstimator
(IMP.isd.TuneRex)
HierarchyVisitor
(
IMP::core
)
ParticleAdaptor
(
IMP
)
SerialMover
(
IMP::core
)
Cylinder3D
(
IMP::algebra
)
HighDensityEmbedding
(
IMP::em
)
ParticleEmbedding
(
IMP::statistics
)
SetCheckState
(
IMP
)
sfo_common
(IMP.isd.shared_functions)
CylinderGeometry
(
IMP::display
)
HistogramD
(
IMP::statistics
)
ParticleIndexAdaptor
(
IMP
)
SetLogState
(
IMP
)
v
vonMises
(
IMP::isd
)
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X