IMP  2.1.0
The Integrative Modeling Platform
File List
Here is a list of all documented files with brief descriptions:
o*algebra/__init__.py
o*atom/__init__.py
o*base/__init__.py
o*benchmark/__init__.py
o*cgal/__init__.py
o*cnmultifit/__init__.py
o*container/__init__.py
o*core/__init__.py
o*display/__init__.py
o*domino/__init__.py
o*em/__init__.py
o*em2d/__init__.py
o*example/__init__.py
o*gsl/__init__.py
o*isd/__init__.py
o*kernel/__init__.py
o*kinematics/__init__.py
o*kmeans/__init__.py
o*misc/__init__.py
o*modeller/__init__.py
o*mpi/__init__.py
o*multifit/__init__.py
o*parallel/__init__.py
o*pepdock/__init__.py
o*restrainer/__init__.py
o*rmf/__init__.py
o*rotamer/__init__.py
o*saxs/__init__.py
o*score_functor/__init__.py
o*scratch/__init__.py
o*statistics/__init__.py
o*symmetry/__init__.py
o*system/__init__.py
o*test/__init__.py
o*_display.py
o*_graph_show.py
o*_histogram.py
o*_interaction_graph.py
o*_main.py
o*_optimization.py
o*_pivy.py
o*_randomize.py
o*_representation.py
o*_restraint.py
o*algebra/_version_check.py
o*atom/_version_check.py
o*base/_version_check.py
o*benchmark/_version_check.py
o*cgal/_version_check.py
o*cnmultifit/_version_check.py
o*container/_version_check.py
o*core/_version_check.py
o*display/_version_check.py
o*domino/_version_check.py
o*em/_version_check.py
o*em2d/_version_check.py
o*example/_version_check.py
o*gsl/_version_check.py
o*isd/_version_check.py
o*kernel/_version_check.py
o*kinematics/_version_check.py
o*kmeans/_version_check.py
o*misc/_version_check.py
o*modeller/_version_check.py
o*mpi/_version_check.py
o*multifit/_version_check.py
o*parallel/_version_check.py
o*pepdock/_version_check.py
o*restrainer/_version_check.py
o*rmf/_version_check.py
o*rotamer/_version_check.py
o*saxs/_version_check.py
o*score_functor/_version_check.py
o*scratch/_version_check.py
o*statistics/_version_check.py
o*symmetry/_version_check.py
o*system/_version_check.py
o*test/_version_check.py
o*_xml_parser.py
o*add_fit_rmsd.py
o*AddScores.hA Score on the distance between a pair of particles
o*algebra.h
o*algebra_config.h
o*algebra_macros.hVarious important macros for implementing geometry
o*align.py
o*align2D.hAlignment of images in 2D Copyright 2007-2013 IMP Inventors. All rights reserved
o*AlignmentParams.hParameters for alignments
o*AlignSymmetric.hFast alignment of a cyclic model to its density
o*AllBipartitePairContainer.hReturn all pairs from a SingletonContainer
o*AllPairContainer.hReturn all pairs from a SingletonContainer
o*AmbiguousNOERestraint.hA lognormal restraint that uses the ISPA model to model NOE-derived distance fit
o*AmbiguousRestraint.hAn implementation of the d-norm to make an ambiguous restraint
o*analysis.hFunctions to get report statistics about the used attributes
o*Analysis.py
o*analyze_convergence.py
o*anchor_graph.hAnchor graph utilities
o*anchor_utilities.hCommon functions in anchor calculations
o*anchors.py
o*anchors_reader.hHandles reading of anchors data
o*angle_decorators.hDecorators for angles
o*AngleRestraint.hAngle restraint between three particles
o*AngleSingletonScore.hA score on the deviation of an angle from ideality
o*AngleTripletScore.hA Score on the angle between three particles
o*argminmax.py
o*base/Array.hClasses to handle static sized arrays of things
o*compatibility/Array.hImport IMP/base/Array.h in the namespace
o*assess_dope.py
o*Assignment.hA beyesian infererence-based sampler
o*assignment_containers.hA beyesian infererence-based sampler
o*assignment_tables.hA beyesian infererence-based sampler
o*associations.hHandle read/write of kernel::Model data from/to files
o*atom/Atom.hSimple atom decorator
o*Atom.h
o*atom_config.h
o*atom_io.hHandle read/write of kernel::Model data from/to files
o*atom_links.hHandle read/write of kernel::Model data from/to files
o*atom_macros.hVarious important macros for implementing decorators
o*atomicDomino.py
o*atomicDominoUtilities.py
o*AttributeOptimizer.hImport IMP/kernel/AttributeOptimizer.h in the namespace
o*kernel/AttributeOptimizer.hBase class for all optimizers
o*AttributeSingletonScore.hA score based on the unmodified value of an attribute
o*core/BallMover.hA modifier which variables within a ball
o*symmetry/BallMover.hA mover that keeps a particle in a box
o*BallMover.py
o*base.h
o*base_config.h
o*base/base_macros.hVarious general useful macros for IMP
o*compatibility/base_macros.hImport IMP/base/base_macros.h in the namespace
o*base_types.hImport IMP/kernel/base_types.h in the namespace
o*kernel/base_types.hBasic types used by IMP
o*basic_display.py
o*basic_geometry.py
o*basic_optimization.py
o*basic_setup.py
o*benchmark.h
o*benchmark_config.h
o*benchmark_macros.hVarious general useful macros for IMP
o*BerendsenThermostatOptimizerState.hMaintains temperature during molecular dynamics using a Berendsen thermostat
o*BildWriter.hWriter for the Chimera BILD file format
o*bipartite_nonbonded_interactions.py
o*bivariate_functions.hClasses for general functions
o*blame.hVarious important functionality for implementing decorators
o*bond_decorators.hContains decorators for a bond
o*bond_graph.hContains decorators for a bond
o*BondedPairFilter.hA fake container for bonds
o*BondEndpointsRefiner.hReturn the endpoints of a bond
o*BondPairContainer.hA fake container for bonds
o*BondSingletonScore.hA Score on the distance between a the two particles in a bond
o*BoundingBox3DSingletonScore.hScore particles based on a bounding box
o*BoundingBoxD.hA bounding box in D dimensions
o*BoxSweepClosePairsFinder.hTest all pairs of particles to find close pairs
o*base/bracket_macros.hVarious general useful macros for IMP
o*compatibility/bracket_macros.hImport IMP/base/bracket_macros.h in the namespace
o*BranchAndBoundSampler.hA beyesian infererence-based sampler
o*brownian_statistics.py
o*BrownianDynamics.hSimple molecular dynamics optimizer
o*build.py
o*buildxlinks.py
o*base/cache.hVarious general useful functions for IMP
o*compatibility/cache.hImport IMP/base/cache.h in the namespace
o*CenteredMat.hDecorator for OpenCV matrix to use relative coordinates Copyright 2007-2013 IMP Inventors. All rights reserved
o*CentroidOfRefined.hSet the coordinates of the particle to be the centoid of the refined particles
o*cg_pdb.py
o*cgal.h
o*cgal_config.h
o*Chain.hStore the chain ID
o*chain.py
o*Charged.hA decorator for a point particle that has an electrostatic charge
o*charmm_forcefield.py
o*charmm_forcefield_verbose.py
o*charmm_segment_topology.hClasses for handling CHARMM-style topology of segments
o*charmm_topology.hClasses for handling CHARMM-style topology
o*CHARMMAtom.hA decorator for an atom that has a defined CHARMM type
o*CHARMMParameters.hAccess to Charmm force field parameters
o*CHARMMStereochemistryRestraint.hClass to maintain CHARMM stereochemistry
o*base/check_macros.hException definitions and assertions
o*compatibility/check_macros.hImport IMP/base/check_macros.h in the namespace
o*ChecksScoreState.hTurn checks on and off
o*ChiFreeScore.hChi free score implementation
o*ChildrenRefiner.hReturn the hierarchy children of a particle
o*chimera_models.py
o*ChimeraWriter.hA writer for Chimera python files
o*ChiScore.hBasic chi score implementation
o*ChiScoreLog.hScoring with log intensity
o*ChiSquareMetric.hChi2 Metric
o*close_pairs_finder_macros.hVarious important macros for implementing decorators
o*CloseBipartitePairContainer.hReturn all pairs from a SingletonContainer
o*ClosedCubicSpline.hClosed cubic spline function
o*ClosePairContainer.hReturn all pairs from a SingletonContainer
o*ClosePairsFinder.hA base class for algorithms to detect proximities
o*ClosePairsPairScore.hApply a PairScore to close pairs
o*cluster.py
o*cluster_coarse.py
o*clustering_macros.hVarious important macros for implementing decorators
o*clustering_of_pdb_models.py
o*CMMWriter.hA writer for chimera CMM files
o*cn_rmsd.hHigh-level functions for RMSD calculation
o*cnmultifit.h
o*cnmultifit_config.h
o*CnSymmAxisDetector.hDetect cn symmetry in proteins and density maps
o*coarse_molecule.hCoarsen molecule by clustering
o*CoarseCC.hPerform coarse fitting between two density objects
o*CoarseCCatIntervals.hCross correlation coefficient calculator
o*CoarseConvolution.hConvolutes two grids
o*collision_cross_section.py
o*CollisionCrossSection.hCopyright 2007-2013 IMP Inventors. All rights reserved
o*Color.hRepresent a color
o*Colored.hA decorator for a particle with a color
o*CommonEndpointPairFilter.hA fake filter that returns true for any pair of bonds with
o*base/comparison_macros.hVarious general useful macros for IMP
o*compatibility/comparison_macros.hImport IMP/base/comparison_macros.h in the namespace
o*compat_subprocess.py
o*compatibility.h
o*base/compiler_macros.hVarious compiler workarounds
o*compatibility/compiler_macros.hImport IMP/base/compiler_macros.h in the namespace
o*ComplementarityRestraint.hCalculate weighted excluded volume between rigid bodies
o*complex_assembly.hA simple unary function
o*CompositeJoint.hJoint composed of several joints, applied on the same pair of rigid bodies
o*Cone3D.hStores a cone
o*Configuration.hImport IMP/kernel/Configuration.h in the namespace
o*kernel/Configuration.hStore a set of configurations of the model
o*ConfigurationSet.hImport IMP/kernel/ConfigurationSet.h in the namespace
o*kernel/ConfigurationSet.hStore a set of configurations of the model
o*core/ConjugateGradients.hSimple conjugate gradients optimizer
o*gsl/ConjugateGradients.hA conjugate gradients optimizer from GSL
o*ConnectingPairContainer.hA container which has pairs which ensure a set is connected
o*connectivity.py
o*connectivity_restraint.py
o*ConnectivityRestraint.hConnectivity restraint
o*connolly_surface.hGenerate surface for a set of atoms
o*ConsecutivePairContainer.hReturn all pairs from a SingletonContainer
o*ConstantRestraint.hConstant restraint
o*algebra/constants.hVarious useful constants
o*atom/constants.hDefine the elements used in IMP
o*constants.hImport IMP/kernel/constants.h in the namespace
o*kernel/constants.hVarious useful constants
o*Constraint.hImport IMP/kernel/Constraint.h in the namespace
o*kernel/Constraint.hA base class for constraints
o*base/ConstVector.hA beyesian infererence-based sampler
o*compatibility/ConstVector.hImport IMP/base/ConstVector.h in the namespace
o*container.h
o*container_base.hImport IMP/kernel/container_base.h in the namespace
o*kernel/container_base.hAbstract base class for containers of particles
o*container_config.h
o*container_macros.hImport IMP/kernel/container_macros.h in the namespace
o*kernel/container_macros.hMacros to define containers of objects
o*converters.hConverters of density values
o*Copy.hA particle with a user-defined type
o*core.h
o*core_config.h
o*core_macros.hVarious important macros for implementing decorators
o*Cosine.hCosine function
o*CoulombPairScore.hCoulomb (electrostatic) score between a pair of particles
o*counting.hA simple unary function
o*cover_particles.py
o*CoverBond.hCover a bond with a sphere
o*CoverRefined.hCover a bond with a sphere
o*base/CreateLogContext.hLogging and error reporting support
o*compatibility/CreateLogContext.hImport IMP/base/CreateLogContext.h in the namespace
o*creating_restraints.hA simple unary function
o*CrossLinkData.hNormal distribution of Function
o*csv_related.py
o*cube.py
o*custom_filter.py
o*custom_hierarchy.py
o*CustomXYZR.hDecorator for a sphere-like particle
o*Cylinder3D.hStores a cylinder
o*CysteineCrossLinkData.hNormal distribution of Function
o*CysteineCrossLinkRestraint.hA sigmoid shaped restraint between residues with discrete classifier and ambiguous assignment. To be used with cross-linking mass-spectrometry data
o*Database.py
o*DataObject.hA modifier which variables within a ball
o*DataPointsAssignment.hTools for data points assignment, after anchor point segmentation
o*decay.py
o*DecayPairContainerOptimizerState.hTrack the particles pairs passed to the pair score
o*declare_Geometry.hImplement geometry for the basic shapes from IMP.algebra
o*declare_Model.hImport IMP/kernel/declare_Model.h in the namespace
o*kernel/declare_Model.hStorage of a model, its restraints, constraints and particles
o*base/declare_Object.hA shared base class to help in debugging and things
o*compatibility/declare_Object.hImport IMP/base/declare_Object.h in the namespace
o*declare_Particle.hImport IMP/kernel/declare_Particle.h in the namespace
o*kernel/declare_Particle.hClasses to handle individual model particles
o*declare_Restraint.hImport IMP/kernel/declare_Restraint.h in the namespace
o*kernel/declare_Restraint.hAbstract base class for all restraints
o*declare_RestraintSet.hImport IMP/kernel/declare_RestraintSet.h in the namespace
o*kernel/declare_RestraintSet.hUsed to hold a set of related restraints
o*declare_ScoringFunction.hImport IMP/kernel/declare_ScoringFunction.h in the namespace
o*kernel/declare_ScoringFunction.hStorage of a model, its restraints, constraints and particles
o*Decorator.hImport IMP/kernel/Decorator.h in the namespace
o*kernel/Decorator.hThe base class for decorators
o*decorator_macros.hImport IMP/kernel/decorator_macros.h in the namespace
o*kernel/decorator_macros.hVarious general useful macros for IMP
o*def.hDefinitions for EMBED
o*density_analysis.hDensity analysis tools, such as histogram and segmentation
o*density_map_volumetrics.hClasses and functions to handle volumetric properties in Density maps
o*density_utilities.hDensity map manipulations
o*density_utils.hDensity utilities
o*DensityDataPoints.hHandling of data for anchor points segmentation
o*DensityFillingRestraint.hScore how well the particles fill the density
o*DensityHeader.hMetadata for a density file
o*DensityMap.hClass for handling density maps
o*dependency_graph.hImport IMP/kernel/dependency_graph.h in the namespace
o*kernel/dependency_graph.hBuild dependency graphs on models
o*dependency_graph.py
o*DependencyScoreState.hA beyesian infererence-based sampler
o*base/deprecation.hControl display of deprecation information
o*compatibility/deprecation.hImport IMP/base/deprecation.h in the namespace
o*base/deprecation_macros.hControl display of deprecation information
o*compatibility/deprecation_macros.hImport IMP/base/deprecation_macros.h in the namespace
o*DerivativeAccumulator.hImport IMP/kernel/DerivativeAccumulator.h in the namespace
o*kernel/DerivativeAccumulator.hClass for adding derivatives from restraints to the model
o*DerivativeCalculator.hA class for computing SAXS derivatives
o*DerivativesFromRefined.hAccumulate the derivatives of the refined particles
o*DerivativesToRefined.hAccumulate the derivatives of the refined particles
o*DiameterRestraint.hA restraint to maintain the diameter of a set of points
o*Diffusion.hA decorator for a diffusing particle
o*DihedralRestraint.hDihedral restraint between four particles
o*dihedrals.hHelpers to extract dihedral information
o*DihedralSingletonScore.hA score on a dihedral angle
o*directional_DOFs.h
o*DiscreteSampler.hA beyesian infererence-based sampler
o*display.h
o*display_config.h
o*display_log.py
o*display_macros.hMacros for display classes
o*displaying_ensembles.py
o*distance.hDistance metrics
o*distance_pair_score_macros.hVarious important macros for implementing decorators
o*core/DistancePairScore.hA Score on the distance between a pair of particles
o*score_functor/DistancePairScore.hA Score on the distance between a pair of particles
o*DistanceRestraint.hDistance restraint between two particles
o*DistanceToSingletonScore.hA Score on the distance to a fixed point
o*DistributePairsScoreState.hApply a PairScore to each Pair in a list
o*DistributeQuadsScoreState.hApply a QuadScore to each Quad in a list
o*DistributeSingletonsScoreState.hApply a SingletonScore to each Singleton in a list
o*DistributeTripletsScoreState.hApply a TripletScore to each Triplet in a list
o*Distribution.hComputes distribution functions
o*DOF.hSingle degree of freedom
o*DOFsSampler.hCopyright 2007-2010 Sali Lab. All rights reserved
o*DOFValues.hSimple class for storage of DOF values
o*Domain.hA decorator for associating an atom::Hierarchy piece with a domain
o*domino.h
o*domino_approach.py
o*domino_config.h
o*domino_filter_tables.hManaging of projection overlap filter
o*domino_filters.hSubsetFilter for checking overlap between projections and images
o*domino_macros.hVarious important macros for implementing decorators
o*domino_particle_states.hKernel::Particles states for a rigid body that is going to be projected
o*DominoModel.py
o*DominoSampler.hA beyesian infererence-based sampler
o*Dope.hA Score on the distance between a pair of particles
o*dope_and_excluded_volume.cpp
o*DopePairScore.hDope scoring
o*doxygen.hImport IMP/kernel/doxygen.h in the namespace
o*kernel/doxygen.hImport kernel classes into the IMP scope in docs
o*base/doxygen_macros.hVarious general useful macros for IMP
o*compatibility/doxygen_macros.hImport IMP/base/doxygen_macros.h in the namespace
o*DummyRestraint.hCopyright 2007-2013 IMP Inventors. All rights reserved
o*DynamicListPairContainer.hStore a list of ParticlePairsTemp
o*DynamicListQuadContainer.hStore a list of ParticleQuadsTemp
o*DynamicListSingletonContainer.hStore a list of ParticlesTemp
o*DynamicListTripletContainer.hStore a list of ParticleTripletsTemp
o*edit_molecular_hierarchy.py
o*eigen_analysis.hPrincipal component analysis of a set of points
o*element.hDefine the elements used in IMP
o*Ellipsoid3D.hSimple 3D ellipsoid class
o*em.h
o*em2d.h
o*em2d_config.h
o*Em2DRestraint.hA restraint to score the fitness of a model to a set of EM images
o*em_config.h
o*em_images_conversion.py
o*em_restraint.py
o*em/embedding.hCluster sets of points
o*statistics/embedding.hCluster sets of points
o*embedding_macros.hVarious important macros for implementing decorators
o*embeddings.hCluster sets of points
o*EMReaderWriter.hClasses to read or write density files in EM format
o*endian.hFunctions to deal with endian of EM images
o*ensemble_analysis.h
o*Entry.py
o*base/enums.hBasic types used by IMP
o*compatibility/enums.hImport IMP/base/enums.h in the namespace
o*envelope_penetration.hFunctions for calculation envelope penetration
o*EnvelopeFitRestraint.hScore envelope fit based on map distance transform
o*EnvelopePenetrationRestraint.hScore how well a protein is inside its density
o*EnvelopeScore.hClass for envelope based scoring using MapDistanceTransform
o*estimates.hEstimates of various physical quantities
o*EventPairsOptimizerState.hDefine some predicates
o*EventQuadsOptimizerState.hDefine some predicates
o*EventSingletonsOptimizerState.hDefine some predicates
o*EventTripletsOptimizerState.hDefine some predicates
o*example.h
o*example_config.h
o*ExampleComplexRestraint.hA restraint to maintain the diameter of a set of points
o*ExampleConstraint.hA restraint on a list of particle pairs
o*ExampleDecorator.hAdd a name to a particle
o*ExampleObject.hAn example showing how to make a simple ref counted object
o*ExamplePairScore.hA Score on the distance between a pair of particles
o*ExampleRestraint.hA restraint on a list of particle pairs
o*ExampleSingletonModifier.hA singleton modifier which wraps an attribute into a given range
o*ExampleSubsetFilterTable.hA Score on the distance between a pair of particles
o*ExampleTemplateClass.hShow how to manage a template class with python
o*ExampleUnaryFunction.hA simple unary function
o*base/exception.hException definitions and assertions
o*compatibility/exception.hImport IMP/base/exception.h in the namespace
o*exception.hImport IMP/kernel/exception.h in the namespace
o*kernel/exception.hFor backwards compatibility
o*excluded_volume.py
o*ExcludedVolumeRestraint.hA prevent spheres from inter-penetrating
o*exp.hAn approximation of the exponential function
o*EzRestraint.hEz potential. A statistical scoring function for atom proteins
o*fft_based_rigid_fitting.hFFT based fitting
o*FFToperations.hOperations involving FFT Copyright 2007-2013 IMP Inventors. All rights reserved
o*base/file.hHandling of file input/output
o*compatibility/file.hImport IMP/base/file.h in the namespace
o*file.hImport IMP/kernel/file.h in the namespace
o*kernel/file.hFor backwards compatibility
o*filenames_manipulation.hGeneration of projections using the central section theorem Copyright 2007-2013 IMP Inventors. All rights reserved
o*filter_close_pairs.py
o*FilterGeometry.hImplement FilterGeometry
o*Fine2DRegistrationRestraint.hAlignment of 2D projections of a 3D volume Copyright 2007-2013 IMP Inventors. All rights reserved
o*fit_fft.py
o*fit_restraint.py
o*FitParameters.hCopyright 2007-2013 IMP Inventors. All rights reserved
o*FitRestraint.hCalculate score based on fit to EM map
o*fitting_solutions_reader_writer.hHandles reading and writing MultiFit fitting solutions file
o*fitting_states.hFitting states
o*fitting_tools.hTools for handling fitting records
o*fitting_utils.hFitting utilities
o*FittingSolutionRecord.hStored a multifit fitting solution
o*FixedRefiner.hA particle refiner which returns a fixed set of particles
o*flags.cpp
o*base/flags.hVarious general useful macros for IMP
o*compatibility/flags.hImport IMP/base/flags.h in the namespace
o*flags.py
o*FloatIndex.hImport IMP/kernel/FloatIndex.h in the namespace
o*kernel/FloatIndex.hVarious general useful functions for IMP
o*FNormal.hNormal distribution of Function
o*force_fields.hDefine functions to add bonds and radii to atoms
o*ForceFieldParameters.hForce field base class
o*FormFactorTable.hA class for computation of atomic and residue level form factors for SAXS calculations
o*Fragment.hA decorator for associating a Hierachy piece
o*frames.hHandle read/write of kernel::Model data from/to files
o*FretData.hAuxiliary class useful for FRET_R restraint
o*FretRestraint.hFRET_R restraint to use in vivo FRET data [Muller et al. Mol Biol Cell 16, 3341, 2005]
o*functor.hImport IMP/kernel/functor.h in the namespace
o*kernel/functor.hVarious important functionality for implementing decorators
o*GaussianProcessInterpolation.hNormal distribution of Function
o*GaussianProcessInterpolationRestraint.hKernel::Restraint and ScoreState for GaussianProcessInterpolation
o*GaussianRestraint.hA lognormal restraint that uses the ISPA model to model NOE-derived distance fit
o*generate_density_map_of_fixed_dimension.py
o*container/generic.hVarious important functionality for implementing decorators
o*core/generic.hVarious important functionality for implementing decorators
o*generic.hImport IMP/kernel/generic.h in the namespace
o*kernel/generic.hVarious important functionality for implementing decorators
o*geometric_alignment.hAlign sets of points
o*geometric_primitive_macros.hVarious important macros for implementing geometry
o*GeometricHash.hGeometric Hashing class
o*GeometricPrimitiveD.hBasic types used by IMP
o*geometry.hBackwards compatibility header
o*algebra/geometry.py
o*rmf/geometry.py
o*geometry_io.hHandle read/write of kernel::Model data from/to files
o*geometry_macros.hMacros for display classes
o*GeometryProcessor.hImplement GeometryProcessor
o*GeometrySet.hImplement geometry for the basic shapes from IMP.algebra
o*graph.py
o*base/graph_macros.hVarious general useful macros for IMP
o*compatibility/graph_macros.hImport IMP/base/graph_macros.h in the namespace
o*grid_embeddings.hA class to represent a voxel grid
o*grid_indexes.hA class to represent a voxel grid
o*grid_ranges.hA class to represent a voxel grid
o*grid_space.py
o*grid_storages.hA class to represent a voxel grid
o*grid_utility.hA class to represent a voxel grid
o*GridClosePairsFinder.hUse a hierarchy of grids to find close pairs
o*GridD.hA class to represent a voxel grid
o*gsl.h
o*gsl_config.h
o*GSLOptimizer.hA base class for GSL-based optimizers
o*core/Harmonic.hHarmonic function
o*score_functor/Harmonic.hA Score on the distance between a pair of particles
o*core/HarmonicLowerBound.hHarmonic lower bound function
o*score_functor/HarmonicLowerBound.hA Score on the distance between a pair of particles
o*core/HarmonicUpperBound.hHarmonic upper bound function
o*score_functor/HarmonicUpperBound.hA Score on the distance between a pair of particles
o*HarmonicWell.hHarmonic function
o*base/hash.hIO support
o*compatibility/hash.hImport IMP/base/hash.h in the namespace
o*base/hash_macros.hVarious general useful macros for IMP
o*compatibility/hash_macros.hImport IMP/base/hash_macros.h in the namespace
o*header_converters.hFunctions to convert between ImageHeader and DensityHeader Copyright 2007-2013 IMP Inventors. All rights reserved
o*hierarchical_clustering.hAgglomerative clustering algorithm
o*atom/Hierarchy.hDecorator for helping deal with a hierarchy of molecules
o*core/Hierarchy.hDecorator for helping deal with a hierarchy
o*hierarchy_tools.hA set of useful functionality on IMP::atom::Hierarchy decorators
o*Histogram.hHolds a histogram
o*HistogramD.hHolds a histogram
o*History.py
o*HybridMonteCarlo.hA hybrid monte carlo implementation
o*Image.hIMP images for Electron Microscopy using openCV matrices Copyright 2007-2013 IMP Inventors. All rights reserved
o*image_processing.hImage processing functions
o*ImageHeader.hHeader for EM images. Compatible with Spider and Xmipp formats Copyright 2007-2013 IMP Inventors. All rights reserved
o*ImageReaderWriter.hVirtual class for reader/writers of images Copyright 2007-2013 IMP Inventors. All rights reserved
o*IMP.h
o*imp_restraints_in_modeller.py
o*ImproperSingletonScore.hA score on the deviation of an improper angle from ideality
o*InContainerPairFilter.hA filter for Pairs
o*InContainerQuadFilter.hA filter for Quads
o*InContainerSingletonFilter.hA filter for Singletons
o*InContainerTripletFilter.hA filter for Triplets
o*incremental_mc.py
o*IncrementalScoringFunction.hSimple Monte Carlo optimizer
o*base/Index.hBasic types used by IMP
o*compatibility/Index.hImport IMP/base/Index.h in the namespace
o*indexes.py
o*input_output.hImport IMP/kernel/input_output.h in the namespace
o*kernel/input_output.hSingle variable function
o*input_output_macros.hImport IMP/kernel/input_output_macros.h in the namespace
o*kernel/input_output_macros.hMacros for inputs and outputs
o*base/InputAdaptor.hBasic types used by IMP
o*compatibility/InputAdaptor.hImport IMP/base/InputAdaptor.h in the namespace
o*interactive.hFunctions to get report statistics about the used attributes
o*interactive.py
o*interactive_with_containers.py
o*algebra/io.hClasses to write entities in algebra to files
o*io.hImport IMP/kernel/io.h in the namespace
o*kernel/io.hHandle read/write of Model data from/to files
o*isd.h
o*isd_config.h
o*JeffreysRestraint.hA restraint on a scale parameter
o*Joint.hFunctionality for defining a kinematic joint between rigid bodies as part of a kinematic tree
o*JPGImageReaderWriter.hManagement of JPG format for EM images Copyright 2007-2013 IMP Inventors. All rights reserved
o*kernel.h
o*kernel_config.h
o*KernelParameters.hCalculates and stores gaussian kernel parameters
o*kernel/Key.hKeys to cache lookup of attribute strings
o*Key.hImport IMP/kernel/Key.h in the namespace
o*kernel/key_macros.hVarious general useful macros for IMP
o*key_macros.hImport IMP/kernel/key_macros.h in the namespace
o*KinematicForest.hWrapper class for a kinematic forest (collection of trees) made of KinematicNode objects, interconnected by joints. This data structure allows for kinematic control of the tree and interconversion between internal and external coordinates
o*KinematicForestScoreState.h
o*KinematicNode.hFunctionality for defining nodes on a kinematic chain
o*kinematics.h
o*kinematics_config.h
o*kmeans/KMeans.hInterface to k-means open source library (stored internally)
o*KMeans.h
o*kmeans.py
o*kmeans_config.h
o*kmeans_example.py
o*LangevinThermostatOptimizerState.hMaintains temperature during molecular dynamics using a Langevin thermostat
o*LeavesRefiner.hReturn the hierarchy children of a particle
o*LennardJones.hA decorator for a particle that has a Lennard-Jones potential well
o*LennardJonesPairScore.hLennard-Jones score between a pair of particles
o*Linear.hA linear function
o*LinearFit.hLinear fit of data points
o*LinearLowerBound.hA Score on the distance between a pair of particles
o*link.py
o*link_macros.hMacros for display classes
o*links.hHandle read/write of kernel::Model data from/to files
o*ListPairContainer.hStore a list of ParticlePairsTemp
o*ListQuadContainer.hStore a list of ParticleQuadsTemp
o*ListSingletonContainer.hStore a list of ParticlesTemp
o*ListTripletContainer.hStore a list of ParticleTripletsTemp
o*base/live_objects.hA shared base class to help in debugging and things
o*compatibility/live_objects.hImport IMP/base/live_objects.h in the namespace
o*load_modeller_model.py
o*load_protein_restrain_bonds.py
o*local_distance.py
o*local_fitting.py
o*local_planners.hPlanners
o*base/log.hLogging and error reporting support
o*compatibility/log.hImport IMP/base/log.h in the namespace
o*kernel/log.hFor backwards compatibility
o*log.hImport IMP/kernel/log.h in the namespace
o*log.py
o*base/log_macros.hLogging and error reporting support
o*compatibility/log_macros.hImport IMP/base/log_macros.h in the namespace
o*LognormalRestraint.hA lognormal restraint that uses the ISPA model to model NOE-derived distance fit
o*LogOptimizerState.hWrite geometry to a file during optimization
o*LogPairScore.hTrack the particles pairs passed to the pair score
o*LowestRefinedPairScore.hScore on the lowest scoring pair of the refined pairs
o*kernel/macros.hVarious general useful macros for IMP
o*macros.hImport IMP/kernel/macros.h in the namespace
o*base/map.hDeclare an efficient stl-compatible map
o*compatibility/map.hImport IMP/base/map.h in the namespace
o*MapDistanceTransform.hClass for computing a distance transform of the density map
o*MapReaderWriter.hAn abstract class for reading a map
o*MarginalHBondRestraint.hA lognormal restraint that uses the ISPA model to model HBond-derived distance fit
o*MarginalNOERestraint.hA lognormal restraint that uses the ISPA model to model NOE-derived distance fit
o*marina_party.py
o*markers.py
o*masking.hMasking tools
o*Mass.hA decorator for particles with mass
o*master_communicator.py
o*base/math.hDeclare an efficient stl-compatible map
o*compatibility/math.hImport IMP/base/math.h in the namespace
o*MCCGSampler.hA Monte Carlo/Conjugate Gradients based sampler
o*doc/examples/domino/merge_tree.py
o*lib/IMP/multifit/merge_tree.py
o*merge_tree_utils.h
o*Metric.hCluster sets of points
o*metric_clustering.hCluster sets of points
o*metric_macros.hVarious important macros for implementing decorators
o*MetricClosePairsFinder.hDecorator for a sphere-like particle
o*metrics.hCluster sets of points
o*MinimumPairRestraint.hScore based on the minimum score over a set of Pairs
o*MinimumPairScore.hDefine PairScore
o*MinimumQuadRestraint.hScore based on the minimum score over a set of Quads
o*MinimumQuadScore.hDefine QuadScore
o*MinimumRestraint.hScore based on the k minimum restraints
o*MinimumSingletonRestraint.hScore based on the minimum score over a set of Singletons
o*MinimumSingletonScore.hDefine SingletonScore
o*MinimumTripletRestraint.hScore based on the minimum score over a set of Triplets
o*MinimumTripletScore.hDefine TripletScore
o*misc.h
o*misc_config.h
o*kernel/Model.hStorage of a model, its restraints, constraints and particles
o*Model.hImport IMP/kernel/Model.h in the namespace
o*model_interaction.hOperations implying interaction of models and the EM module
o*kernel/model_object_helpers.hSingle variable function
o*model_object_helpers.hImport IMP/kernel/model_object_helpers.h in the namespace
o*model_statistics.hLog the restraint scores and things
o*modeller.h
o*modeller_config.h
o*modeller_restraints_in_imp.py
o*kernel/ModelObject.hSingle variable function
o*ModelObject.hImport IMP/kernel/ModelObject.h in the namespace
o*models.py
o*mol2.hFunctions to read mol2s
o*MolCnSymmAxisDetector.hMolecule symmetry detector
o*molecular_hierarchy.py
o*atom/MolecularDynamics.hSimple molecular dynamics optimizer
o*isd/MolecularDynamics.hSimple molecular dynamics optimizer
o*MolecularDynamicsMover.hA modifier which perturbs XYZs or Nuisances with a constant energy MD simulation
o*Molecule.hA decorator for Molecules
o*monte_carlo_macros.hVarious important macros for implementing decorators
o*MonteCarlo.hSimple Monte Carlo optimizer
o*MonteCarloMover.hThe base class for movers for MC optimization
o*MonteCarloRelativeMoves.py
o*Mover.hBackwards compatibility
o*mover_macros.hBackwards compatibility
o*MoverBase.hBackwards compatibility
o*MoveStatisticsScoreState.hWrite geometry to a file during optimization
o*mpi.h
o*mpi_config.h
o*MRCReaderWriter.hClasses to read or write MRC files
o*ms_connectivity_restraint.py
o*MSConnectivityRestraint.hMass Spec Connectivity restraint
o*multifit.h
o*multifit_config.h
o*MultipleBinormalRestraint.hKernel::Modeller-style multiple binormal (phi/psi) restraint
o*multiresolution.py
o*multiscale.py
o*MultivariateFNormalSufficient.hNormal distribution of Function
o*NearestNeighborsClosePairsFinder.hTest all pairs of particles to find close pairs
o*NeighborsTable.hAngle restraint between three particles
o*NOERestraint.hA lognormal restraint that uses the ISPA model to model NOE-derived distance fit
o*nonbonded_interactions.py
o*base/NonCopyable.hBasic types used by IMP
o*compatibility/NonCopyable.hImport IMP/base/NonCopyable.h in the namespace
o*NormalMover.hA modifier which perturbs a point with a normal distribution
o*Nuisance.hA decorator for nuisance parameters particles
o*base/nullptr.hProvide a nullptr keyword analog
o*compatibility/nullptr.hImport IMP/base/nullptr.h in the namespace
o*base/nullptr_macros.hProvide a nullptr keyword analog
o*compatibility/nullptr_macros.hImport IMP/base/nullptr_macros.h in the namespace
o*nup84.py
o*nup84_complex_in_bead_representation.py
o*base/Object.hA shared base class to help in debugging and things
o*compatibility/Object.hImport IMP/base/Object.h in the namespace
o*kernel/Object.hA shared base class to help in debugging and things
o*Object.hImport IMP/kernel/Object.h in the namespace
o*base/object_cast.hA shared base class to help in debugging and things
o*compatibility/object_cast.hImport IMP/base/object_cast.h in the namespace
o*base/object_macros.hVarious general useful macros for IMP
o*compatibility/object_macros.hImport IMP/base/object_macros.h in the namespace
o*core/OpenCubicSpline.hOpen cubic spline function
o*score_functor/OpenCubicSpline.hA Score on the distance between a pair of particles
o*opencv_interface.hInteface with OpenCV Copyright 2007-2013 IMP Inventors. All rights reserved
o*optimize_balls.py
o*optimize_em2d_with_montecarlo.py
o*kernel/Optimizer.hBase class for all optimizers
o*Optimizer.hImport IMP/kernel/Optimizer.h in the namespace
o*kernel/optimizer_macros.hVarious general useful macros for IMP
o*optimizer_macros.hImport IMP/kernel/optimizer_macros.h in the namespace
o*kernel/optimizer_state_macros.hVarious general useful macros for IMP
o*optimizer_state_macros.hImport IMP/kernel/optimizer_state_macros.h in the namespace
o*kernel/OptimizerState.hShared optimizer state
o*OptimizerState.hImport IMP/kernel/OptimizerState.h in the namespace
o*optimizing.hA simple unary function
o*Order.hA beyesian infererence-based sampler
o*osPeptideDocker.py
o*kernel/pair_macros.hMacros for various classes
o*pair_macros.hImport IMP/kernel/pair_macros.h in the namespace
o*pair_predicates.hDefine some predicates
o*pair_restraint.py
o*PairConstraint.hUse a PairModifier applied to a ParticlePairsTemp to maintain an invariant
o*kernel/PairContainer.hA container for Pairs
o*PairContainer.hImport IMP/kernel/PairContainer.h in the namespace
o*PairContainerSet.hStore a set of PairContainers
o*PairContainerStatistics.hA container for Pairs
o*kernel/PairDerivativeModifier.hA Modifier on ParticlePairsTemp
o*PairDerivativeModifier.hImport IMP/kernel/PairDerivativeModifier.h in the namespace
o*kernel/PairModifier.hA Modifier on ParticlePairsTemp
o*PairModifier.hImport IMP/kernel/PairModifier.h in the namespace
o*kernel/PairPredicate.hDefine PairPredicate
o*PairPredicate.hImport IMP/kernel/PairPredicate.h in the namespace
o*PairRestraint.hApply a PairScore to a Pair
o*PairsConstraint.hUse a PairModifier applied to a ParticlePairsTemp to maintain an invariant
o*kernel/PairScore.hDefine PairScore
o*PairScore.hImport IMP/kernel/PairScore.h in the namespace
o*PairsOptimizerState.hUse a PairModifier applied to a ParticlePairsTemp to maintain an invariant
o*PairsRestraint.hApply a PairScore to each Pair in a list
o*ParabolicFit.hFit the data with parabola
o*parallel.h
o*parallel_config.h
o*cnmultifit/param.py
o*multifit/param.py
o*kernel/Particle.hClasses to handle individual model particles
o*Particle.hImport IMP/kernel/Particle.h in the namespace
o*particle_geometry.hRepresent an XYZR particle with a sphere
o*kernel/particle_index.hVarious general useful functions for IMP
o*particle_index.hImport IMP/kernel/particle_index.h in the namespace
o*particle_io.hHandle read/write of kernel::Model data from/to files
o*particle_states.hA beyesian infererence-based sampler
o*kernel/ParticleTuple.hClasses to handle individual model particles
o*ParticleTuple.hImport IMP/kernel/ParticleTuple.h in the namespace
o*partitional_clustering_macros.hVarious important macros for implementing decorators
o*PartitionalClustering.hCompute a distance metric between two points
o*PartitionalClusteringWithCenter.hCluster sets of points
o*path_reader_writer.hRead and write paths
o*pca_based_rigid_fitting.hPreforms rigid fitting between a set of particles and a density map
o*PCAAligner.hCopyright 2007-2013 IMP Inventors. All rights reserved
o*PCAFitRestraint.hCalculate match between density map PCA and particles PCA
o*pdb.hFunctions to read pdbs
o*pdb.py
o*pdb2density.py
o*pepdock.h
o*pepdock_config.h
o*peptideDocker.py
o*periodic_optimizer_state_macros.hVarious important macros for implementing decorators
o*PeriodicOptimizerState.hAngle restraint between three particles
o*base/piecewise_linear_distribution.hBoost piecewise linear
o*compatibility/piecewise_linear_distribution.hImport IMP/base/piecewise_linear_distribution.h in the namespace
o*Plane3D.hSimple 3D plane class
o*point_clustering.hCluster sets of points
o*base/Pointer.hA nullptr-initialized pointer to an IMP Object
o*compatibility/Pointer.hImport IMP/base/Pointer.h in the namespace
o*kernel/Pointer.hFor backwards compatibility
o*Pointer.hImport IMP/kernel/Pointer.h in the namespace
o*PolarResamplingParameters.hFuntions related with rotations in em2d Copyright 2007-2013 IMP Inventors. All rights reserved
o*PredicatePairsRestraint.hApply a PairScore to each Pair in a list
o*PredicateQuadsRestraint.hApply a QuadScore to each Quad in a list
o*predicates.hScore particles based on a bounding box
o*PredicateSingletonsRestraint.hApply a SingletonScore to each Singleton in a list
o*PredicateTripletsRestraint.hApply a TripletScore to each Triplet in a list
o*primitive_geometries.hImplement geometry for the basic shapes from IMP.algebra
o*PrismaticJoint.hPrismatic joint between rigid bodies as part of a kinematic tree
o*Profile.hA class for profile storing and computation
o*profile.py
o*profile_fit.py
o*ProfileFitter.hClass for fitting two profiles
o*Profiler.hVarious utilities for benchmarking
o*project.hGeneration of projections from models or density maps Copyright 2007-2013 IMP Inventors. All rights reserved
o*ProjectionFinder.hCoarse registration of 2D projections from a 3D volume
o*ProjectionMask.hProjection masks Copyright 2007-2013 IMP Inventors. All rights reserved
o*ProjectionParameters.hDecorator for projection parameters Copyright 2007-2013 IMP Inventors. All rights reserved
o*protein_anchors_mapping_reader.hHandles reading matches between a protein and its anchors
o*protein_ligand_score.hFunctions to read mol2s
o*ProteinKinematics.hFunctionality for defining a kinematic forest for proteins
o*proteomics.py
o*proteomics_em_alignment_atomic.hAlign proteomics graph to em density map
o*proteomics_reader.hHandles reading of proteomics data
o*PymolWriter.hImplement PymolWriter
o*algebra/python_only.hFunctionality only availble in python
o*atom/python_only.hFunctionality only availble in python
o*core/python_only.hFunctionality only availble in python
o*display/python_only.hBuild dependency graphs on models
o*kernel/python_only.hBuild dependency graphs on models
o*python_only.hImport IMP/kernel/python_only.h in the namespace
o*statistics/python_only.hPython-only functionality
o*kernel/quad_macros.hMacros for various classes
o*quad_macros.hImport IMP/kernel/quad_macros.h in the namespace
o*quad_predicates.hDefine some predicates
o*QuadConstraint.hUse a QuadModifier applied to a ParticleQuadsTemp to maintain an invariant
o*kernel/QuadContainer.hA container for Quads
o*QuadContainer.hImport IMP/kernel/QuadContainer.h in the namespace
o*QuadContainerSet.hStore a set of QuadContainers
o*QuadContainerStatistics.hA container for Quads
o*kernel/QuadDerivativeModifier.hA Modifier on ParticleQuadsTemp
o*QuadDerivativeModifier.hImport IMP/kernel/QuadDerivativeModifier.h in the namespace
o*kernel/QuadModifier.hA Modifier on ParticleQuadsTemp
o*QuadModifier.hImport IMP/kernel/QuadModifier.h in the namespace
o*kernel/QuadPredicate.hDefine QuadPredicate
o*QuadPredicate.hImport IMP/kernel/QuadPredicate.h in the namespace
o*QuadraticClosePairsFinder.hTest all pairs of particles to find close pairs
o*QuadRestraint.hApply a QuadScore to a Quad
o*QuadsConstraint.hUse a QuadModifier applied to a ParticleQuadsTemp to maintain an invariant
o*kernel/QuadScore.hDefine QuadScore
o*QuadScore.hImport IMP/kernel/QuadScore.h in the namespace
o*QuadsOptimizerState.hUse a QuadModifier applied to a ParticleQuadsTemp to maintain an invariant
o*QuadsRestraint.hApply a QuadScore to each Quad in a list
o*QuasiNewton.hA GSL-based Quasi-Newton optimizer
o*multifit/RadiusOfGyrationRestraint.hRadius of gyration restraint
o*saxs/RadiusOfGyrationRestraint.hCalculate score based on fit to SAXS profile
o*base/RAII.hBasic types used by IMP
o*compatibility/RAII.hImport IMP/base/RAII.h in the namespace
o*base/raii_macros.hVarious general useful macros for IMP
o*compatibility/raii_macros.hImport IMP/base/raii_macros.h in the namespace
o*base/random.hRandom number generators used by IMP
o*compatibility/random.hImport IMP/base/random.h in the namespace
o*kernel/random.hFor backwards compatibility
o*random.hImport IMP/kernel/random.h in the namespace
o*randomize_rigid_body.py
o*randomizing.hA simple unary function
o*range_restriction.py
o*RecursivePartitionalClusteringEmbedding.hCluster sets of points
o*RecursivePartitionalClusteringMetric.hCluster sets of points
o*base/ref_counted_macros.hVarious general useful macros for IMP
o*compatibility/ref_counted_macros.hImport IMP/base/ref_counted_macros.h in the namespace
o*base/RefCounted.hA common base class for ref counted objects
o*compatibility/RefCounted.hImport IMP/base/RefCounted.h in the namespace
o*kernel/RefCounted.hFor backwards compatibility
o*RefCounted.hImport IMP/kernel/RefCounted.h in the namespace
o*reference.py
o*ReferenceFrame3D.hSimple 3D rotation class
o*refine_fft.py
o*RefinedPairsPairScore.hGenerate pairs by applying a Refiner to the paricles
o*kernel/Refiner.hRefine a particle into a list of particles
o*Refiner.hImport IMP/kernel/Refiner.h in the namespace
o*kernel/refiner_macros.hVarious general useful macros for IMP
o*refiner_macros.hImport IMP/kernel/refiner_macros.h in the namespace
o*Reflection3D.hReflect about a plane in 3D
o*RegistrationResult.hRegistration results class Copyright 2007-2013 IMP Inventors. All rights reserved
o*RelativePositionMover.hMover for Rigid Bodies moving respect to each other
o*RemoveRigidMotionOptimizerState.hRemove rigid rotation and translation during molecular dynamics
o*RemoveTranslationOptimizerState.hRemove rigid translation during optimization
o*Replica.py
o*ReplicaExchange.hA class to do replica exchange in a generic hamiltonian parameter
o*RepulsiveDistancePairScore.hA simple quadric repulsive term between two atoms. Restraint is zero when the distance equals the sum of the radii plus the shift
o*Residue.hA decorator for Residues
o*restrain_diameter.py
o*container/restrain_in_sphere.py
o*core/restrain_in_sphere.py
o*restrain_minimum_distance.py
o*restrainer.h
o*restrainer_config.h
o*kernel/Restraint.hAbstract base class for all restraints
o*Restraint.hImport IMP/kernel/Restraint.h in the namespace
o*saxs/Restraint.hCalculate score based on fit to SAXS profile
o*restraint_cache.py
o*restraint_geometry.hRepresent an XYZR restraint with a sphere
o*restraint_io.hHandle read/write of kernel::Model data from/to files
o*kernel/restraint_macros.hVarious general useful macros for IMP
o*restraint_macros.hImport IMP/kernel/restraint_macros.h in the namespace
o*restraints.py
o*kernel/RestraintSet.hUsed to hold a set of related restraints
o*RestraintSet.hImport IMP/kernel/RestraintSet.h in the namespace
o*RestraintsScoringFunction.hStorage of a model, its restraints, constraints and particles
o*revolute_joints.hFunctionality for defining various revolute kinematic joints between rigid bodies as part of a kinematic tree, including RevoluteJoint, DihedralAngleRevoluteJoint, and BondAngleRevoluteJoint
o*rigid_bodies.hFunctionality for defining rigid bodies
o*rigid_bodies.py
o*rigid_body_and_excluded_volume_restraint.py
o*rigid_body_excluded_volume.py
o*rigid_body_geometries.hFunctionality for defining rigid bodies
o*rigid_brownian_dynamics.py
o*rigid_collisions.py
o*rigid_fitting.hPreforms rigid fitting between a set of particles and a density map
o*RigidBodiesImageFitRestraint.hFit kernel::Restraint
o*RigidBodyDistancePairScore.hAct on the distance between two rigid bodies
o*core/RigidBodyMover.hA mover that transform a rigid body
o*symmetry/RigidBodyMover.hA mover that keeps a rigid body in a box
o*RigidClosePairsFinder.hHandle rigid bodies by looking at their members
o*rmf.h
o*rmf_config.h
o*RMFWriter.hHandle read/write of kernel::Model data from/to files
o*rmsd.py
o*rotamer.h
o*rotamer_config.h
o*rotamer_pdb.py
o*rotamer_pdb2.py
o*RotamerCalculator.hObject performing rotations by Chi angles
o*RotamerLibrary.hObject representing rotamer library
o*Rotation2D.hClasses and operations related with rotations
o*Rotation3D.hSimple 3D rotation class
o*RRT.hSimple RRT implementation
o*SameResiduePairFilter.hA Score on the distance between a pair of particles
o*SampledDensityMap.hSampled density map
o*kernel/Sampler.hBase class for all samplers
o*Sampler.hImport IMP/kernel/Sampler.h in the namespace
o*kernel/sampler_macros.hVarious general useful macros for IMP
o*sampler_macros.hImport IMP/kernel/sampler_macros.h in the namespace
o*sampling.py
o*save_assignments.py
o*SaveOptimizerState.hHandle read/write of kernel::Model data from/to files
o*saxs.h
o*saxs_config.h
o*saxs_restraint.py
o*Scale.hA decorator for scale parameters particles
o*kernel/scoped.hVarious general useful functions for IMP
o*scoped.hImport IMP/kernel/scoped.h in the namespace
o*Score.hA Score on the distance between a pair of particles
o*score.py
o*score_functor.h
o*score_functor_config.h
o*score_protein_with_ligand.py
o*kernel/score_state_macros.hVarious general useful macros for IMP
o*score_state_macros.hImport IMP/kernel/score_state_macros.h in the namespace
o*kernel/ScoreAccumulator.hClass for adding scores from restraints to the model
o*ScoreAccumulator.hImport IMP/kernel/ScoreAccumulator.h in the namespace
o*scores2D.hScoring functions for 2D Copyright 2007-2013 IMP Inventors. All rights reserved
o*kernel/ScoreState.hShared score state
o*ScoreState.hImport IMP/kernel/ScoreState.h in the namespace
o*ScoreUnaryFunction.hA Score on the distance between a pair of particles
o*kernel/scoring_function_macros.hVarious general useful macros for IMP
o*scoring_function_macros.hImport IMP/kernel/scoring_function_macros.h in the namespace
o*kernel/ScoringFunction.hStorage of a model, its restraints, constraints and particles
o*ScoringFunction.hImport IMP/kernel/ScoringFunction.h in the namespace
o*scratch.h
o*scratch_config.h
o*secondary_structure_reader.hFunctions to read PSIPRED/DSSP and encode as SSES
o*SecondaryStructureResidue.hA decorator for storing secondary structure probabilities. Copyright 2007-2013 IMP Inventors. All rights reserved
o*segment.py
o*Segment3D.hSimple implementation of segments in 3D
o*Selection.hA set of useful functionality on IMP::atom::Hierarchy decorators
o*SerialMover.hA mover that apply other movers one at a time
o*serialPeptideDocker.py
o*base/set.hDeclare an efficient stl-compatible set
o*compatibility/set.hImport IMP/base/set.h in the namespace
o*base/SetCheckState.hCheckging and error reporting support
o*compatibility/SetCheckState.hImport IMP/base/SetCheckState.h in the namespace
o*base/SetLogState.hLogging and error reporting support
o*compatibility/SetLogState.hImport IMP/base/SetLogState.h in the namespace
o*SettingsData.hStored multifit settings data
o*setup.py
o*shared_functions.py
o*Shift.hA Score on the distance between a pair of particles
o*shortest_segment.hPredicates implemented using CGAL Copyright 2007-2013 IMP Inventors. All rights reserved
o*show_particles_as_spheres.py
o*base/Showable.hIO support
o*compatibility/Showable.hImport IMP/base/Showable.h in the namespace
o*base/showable_macros.hVarious general useful macros for IMP
o*compatibility/showable_macros.hImport IMP/base/showable_macros.h in the namespace
o*simple.cpp
o*simple.py
o*simple_connectivity_on_molecules.py
o*simple_connectivity_on_rigid_bodies.py
o*simple_diameter.py
o*simple_distance.py
o*simple_em_fit.py
o*simple_excluded_volume.py
o*simple_links.hHandle read/write of kernel::Model data from/to files
o*Simplex.hThe simplex algorithm from GSL
o*simplex.py
o*simplify_restraint.hRestrainer functions for restraints
o*simulation.py
o*Simulator.hSimple molecular dynamics optimizer
o*kernel/singleton_macros.hMacros for various classes
o*singleton_macros.hImport IMP/kernel/singleton_macros.h in the namespace
o*singleton_predicates.hDefine some predicates
o*SingletonConstraint.hUse a SingletonModifier applied to a ParticlesTemp to maintain an invariant
o*kernel/SingletonContainer.hA container for Singletons
o*SingletonContainer.hImport IMP/kernel/SingletonContainer.h in the namespace
o*SingletonContainerSet.hStore a set of SingletonContainers
o*SingletonContainerStatistics.hA container for Singletons
o*kernel/SingletonDerivativeModifier.hA Modifier on ParticlesTemp
o*SingletonDerivativeModifier.hImport IMP/kernel/SingletonDerivativeModifier.h in the namespace
o*kernel/SingletonModifier.hA Modifier on ParticlesTemp
o*SingletonModifier.hImport IMP/kernel/SingletonModifier.h in the namespace
o*kernel/SingletonPredicate.hDefine SingletonPredicate
o*SingletonPredicate.hImport IMP/kernel/SingletonPredicate.h in the namespace
o*SingletonRestraint.hApply a SingletonScore to a Singleton
o*SingletonsConstraint.hUse a SingletonModifier applied to a ParticlesTemp to maintain an invariant
o*kernel/SingletonScore.hDefine SingletonScore
o*SingletonScore.hImport IMP/kernel/SingletonScore.h in the namespace
o*SingletonsOptimizerState.hUse a SingletonModifier applied to a ParticlesTemp to maintain an invariant
o*SingletonsRestraint.hApply a SingletonScore to each Singleton in a list
o*SingletonStatistical.hStatistical score for a single particle based on one parameter, such as solvent accessability
o*six_particles_optimization.py
o*slave_handler.py
o*slavestate.py
o*Slice.hA beyesian infererence-based sampler
o*smoothing_functions.hClasses to smooth nonbonded interactions
o*Soap.hA Score on the distance between a pair of particles
o*SoftCylinderPairScore.hA Score on the distance between a pair of particles
o*solutions_io.py
o*SolventAccessibleSurface.hCopyright 2007-2013 IMP Inventors. All rights reserved
o*Sphere3D.hSimple 3D sphere class
o*SphereD.hSimple 3D sphere class
o*SphereDistance.hA Score on the distance between a pair of particles
o*SphereDistancePairScore.hA score on the distance between the surfaces of two spheres
o*SpherePatch3D.hSimple 3D sphere patch class
o*SphericalVector3D.hStores and converts spherical coordinates
o*SpiderHeader.hHeader for Spider and Xmipp formats
o*SpiderImageReaderWriter.hManagement of Images in Spider format Copyright 2007-2013 IMP Inventors. All rights reserved
o*SpiderReaderWriter.hManagement of Spider Headers Electron Microscopy. Compatible with Spider and Xmipp formats Copyright 2007-2013 IMP Inventors. All rights reserved
o*standard_grids.hA class to represent a voxel grid
o*StateAdaptor.hXXXXXXXXXXXXXX
o*Statistical.hA Score on the distance between a pair of particles
o*StatisticalPairScore.hFunctions to read mol2s
o*base/statistics.hManage statistics on IMP runs
o*compatibility/statistics.hImport IMP/base/statistics.h in the namespace
o*statistics.h
o*Statistics.py
o*statistics_config.h
o*SteepestDescent.hSimple steepest descent optimizer
o*StereochemistryPairFilter.hA filter that excludes bonds, angles and dihedrals
o*structure_from_sequence.py
o*subproc.py
o*Subset.hA beyesian infererence-based sampler
o*subset_filters.hA beyesian infererence-based sampler
o*subset_graphs.hA beyesian infererence-based sampler
o*subset_scores.hA beyesian infererence-based sampler
o*surface.py
o*SurfaceShellDensityMap.hRepresent a molecule as shells of distance from the surface
o*base/swap_macros.hVarious general useful macros for IMP
o*compatibility/swap_macros.hImport IMP/base/swap_macros.h in the namespace
o*base/swig_macros.hVarious general useful macros for IMP
o*compatibility/swig_macros.hImport IMP/base/swig_macros.h in the namespace
o*Switching.hA decorator for switching parameters particles
o*symmetric_multifit.hBuild cyclic symmetric complexes
o*core/symmetry.hImplement various types of symmetry
o*symmetry.h
o*symmetry.py
o*symmetry_config.h
o*symmetry_utils.hSymmetry utilities
o*system.h
o*system_config.h
o*TableRefiner.hA lookup based particle refiner
o*TALOSReader.py
o*TALOSRestraint.hTALOS dihedral restraint between four particles
o*tasks.py
o*TBLReader.py
o*temperature_rem.py
o*test.h
o*test_config.h
o*test_macros.h
o*base/thread_macros.hControl for OpenMP
o*compatibility/thread_macros.hImport IMP/base/thread_macros.h in the namespace
o*base/threads.hControl for using multiple threads in IMP
o*compatibility/threads.hImport IMP/base/threads.h in the namespace
o*TIFFImageReaderWriter.hManagement of reading/writing TIFF images
o*Transform.hTransform a particle
o*Transformation2D.h2D transformations. Copyright 2007-2013 IMP Inventors. All rights reserved
o*Transformation3D.hSimple 3D transformation class
o*TransformationJoint.hKinematic joints between rigid bodies that allows any transformation
o*TransformedDistancePairScore.hA score on the distance between a pair of particles after transforming one
o*transforms.py
o*Triangle3D.hSimple implementation of a triangle in 3D
o*kernel/triplet_macros.hMacros for various classes
o*triplet_macros.hImport IMP/kernel/triplet_macros.h in the namespace
o*triplet_predicates.hDefine some predicates
o*TripletConstraint.hUse a TripletModifier applied to a ParticleTripletsTemp to maintain an invariant
o*kernel/TripletContainer.hA container for Triplets
o*TripletContainer.hImport IMP/kernel/TripletContainer.h in the namespace
o*TripletContainerSet.hStore a set of TripletContainers
o*TripletContainerStatistics.hA container for Triplets
o*kernel/TripletDerivativeModifier.hA Modifier on ParticleTripletsTemp
o*TripletDerivativeModifier.hImport IMP/kernel/TripletDerivativeModifier.h in the namespace
o*kernel/TripletModifier.hA Modifier on ParticleTripletsTemp
o*TripletModifier.hImport IMP/kernel/TripletModifier.h in the namespace
o*kernel/TripletPredicate.hDefine TripletPredicate
o*TripletPredicate.hImport IMP/kernel/TripletPredicate.h in the namespace
o*TripletRestraint.hApply a TripletScore to a Triplet
o*TripletsConstraint.hUse a TripletModifier applied to a ParticleTripletsTemp to maintain an invariant
o*kernel/TripletScore.hDefine TripletScore
o*TripletScore.hImport IMP/kernel/TripletScore.h in the namespace
o*TripletsOptimizerState.hUse a TripletModifier applied to a ParticleTripletsTemp to maintain an invariant
o*TripletsRestraint.hApply a TripletScore to each Triplet in a list
o*TruncatedHarmonic.hTruncated harmonic
o*TuneRex.py
o*base/tuple_macros.hVarious general useful macros for IMP
o*compatibility/tuple_macros.hImport IMP/base/tuple_macros.h in the namespace
o*Typed.hA particle with a user-defined type
o*TypedPairScore.hDelegate to another PairScore depending on particle types
o*base/types.hBasic types used by IMP
o*compatibility/types.hImport IMP/base/types.h in the namespace
o*kernel/unary_function_macros.hVarious general useful macros for IMP
o*unary_function_macros.hImport IMP/kernel/unary_function_macros.h in the namespace
o*kernel/UnaryFunction.hSingle variable function
o*UnaryFunction.hImport IMP/kernel/UnaryFunction.h in the namespace
o*UnaryFunctionEvaluate.hA Score on the distance between a pair of particles
o*kernel/Undecorator.hThe base class for decorators
o*Undecorator.hImport IMP/kernel/Undecorator.h in the namespace
o*UniformBackboneSampler.hA class for uniform sampling of backbone angles
o*univariate_functions.hClasses for general functions
o*util.py
o*algebra/utility.hFunctions to deal with very common math operations
o*base/utility.hVarious general useful functions for IMP
o*benchmark/utility.hVarious utilities for benchmarking
o*compatibility/utility.hImport IMP/base/utility.h in the namespace
o*core/utility.hVarious important functionality for implementing decorators
o*domino/utility.hFunctions to get report statistics about the used attributes
o*kernel/utility.hFor backwards compatibility
o*saxs/utility.hFunctions to deal with very common saxs operations Copyright 2007-2013 IMP Inventors. All rights reserved
o*statistics/utility.hCluster sets of points
o*utility.hImport IMP/kernel/utility.h in the namespace
o*utility.py
o*base/utility_macros.hVarious general useful macros for IMP
o*compatibility/utility_macros.hImport IMP/base/utility_macros.h in the namespace
o*utils.py
o*base/Value.hBasic types used by IMP
o*compatibility/Value.hImport IMP/base/Value.h in the namespace
o*base/value_macros.hVarious general useful macros for IMP
o*compatibility/value_macros.hImport IMP/base/value_macros.h in the namespace
o*base/Vector.hA class for storing lists of IMP items
o*compatibility/Vector.hImport IMP/base/Vector.h in the namespace
o*Vector2D.hSimple 2D vector class
o*Vector3D.hSimple 3D vector class
o*vector_generators.hFunctions to generate vectors
o*vector_metrics.hFunctions to generate vectors
o*base/vector_property_map.hInclude the correct headers to get the boost vector_property_map
o*compatibility/vector_property_map.hImport IMP/base/vector_property_map.h in the namespace
o*vector_search.hFunctions to generate vectors
o*VectorD.hSimple D vector class
o*VelocityScalingOptimizerState.hMaintains temperature during molecular dynamics by velocity scaling
o*base/VersionInfo.hVersion and authorship of IMP objects
o*compatibility/VersionInfo.hImport IMP/base/VersionInfo.h in the namespace
o*kernel/VersionInfo.hVersion and authorship of IMP objects
o*VersionInfo.hImport IMP/kernel/VersionInfo.h in the namespace
o*VolumeRestraint.hA prevent spheres from inter-penetrating
o*vonMises.hNormal distribution of Function
o*vonMisesKappaConjugateRestraint.hConjugate prior for \(\kappa\) in the von Mises distribution
o*vonMisesKappaJeffreysRestraint.hJeffreys prior for \(\kappa\) in the von Mises distribution
o*vonMisesSufficient.hNormal distribution of Function
o*Voxel.hVoxel decorator
o*base/warning_macros.hVarious general useful macros for IMP
o*compatibility/warning_macros.hImport IMP/base/warning_macros.h in the namespace
o*base/WarningContext.hLogging and error reporting support
o*compatibility/WarningContext.hImport IMP/base/WarningContext.h in the namespace
o*base/WeakPointer.hA nullptr-initialized pointer to an Object
o*compatibility/WeakPointer.hImport IMP/base/WeakPointer.h in the namespace
o*kernel/WeakPointer.hFor backwards compatibility
o*WeakPointer.hImport IMP/kernel/WeakPointer.h in the namespace
o*Weight.hAdd weights for a set of states to a particle
o*weighted_excluded_volume.hHandles low resolution weighted excluded volume calculation
o*WeightedExcludedVolumeRestraint.hCalculate weighted excluded volume between rigid bodies
o*WeightedFitParameters.hCopyright 2007-2013 IMP Inventors. All rights reserved
o*WeightedProfileFitter.hFitting of multiple profiles to the experimental one. The weights of the profiles are computed analytically using non-negative least squares fitting (NNLS)
o*WeightMover.hA mover that transform a rigid body
o*WeightRestraint.hPut description here
o*WeightScore.hA Score on the distance between a pair of particles
o*WormLikeChain.hWorm-like-chain score for polymer chains
o*write_a_metric.py
o*write_a_restraint.py
o*write_an_optimizer_state.py
o*Writer.hBase class for writing geometry to a file
o*writer_macros.hMacros for display classes
o*XplorReaderWriter.hClasses to read or write density files in XPLOR format
o*XYZ.hSimple xyz decorator
o*XYZ_Decorator.py
o*XYZR.hDecorator for a sphere-like particle
\*XYZR_Decorator.py