IMP
2.0.0
The Integrative Modeling Platform
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__init__.py | |
algebra/__init__.py | |
atom/__init__.py | |
base/__init__.py | |
benchmark/__init__.py | |
cgal/__init__.py | |
cnmultifit/__init__.py | |
container/__init__.py | |
core/__init__.py | |
display/__init__.py | |
domino/__init__.py | |
em/__init__.py | |
em2d/__init__.py | |
example/__init__.py | |
gsl/__init__.py | |
isd/__init__.py | |
kernel/__init__.py | |
kmeans/__init__.py | |
misc/__init__.py | |
modeller/__init__.py | |
multifit/__init__.py | |
parallel/__init__.py | |
pepdock/__init__.py | |
restrainer/__init__.py | |
rmf/__init__.py | |
rotamer/__init__.py | |
saxs/__init__.py | |
score_functor/__init__.py | |
scratch/__init__.py | |
statistics/__init__.py | |
system/__init__.py | |
test/__init__.py | |
_display.py | |
_graph_show.py | |
_histogram.py | |
_interaction_graph.py | |
_main.py | |
_optimization.py | |
_pivy.py | |
_randomize.py | |
_representation.py | |
_restraint.py | |
algebra/_version_check.py | |
atom/_version_check.py | |
base/_version_check.py | |
benchmark/_version_check.py | |
cgal/_version_check.py | |
cnmultifit/_version_check.py | |
container/_version_check.py | |
core/_version_check.py | |
display/_version_check.py | |
domino/_version_check.py | |
em/_version_check.py | |
em2d/_version_check.py | |
example/_version_check.py | |
gsl/_version_check.py | |
isd/_version_check.py | |
kernel/_version_check.py | |
kmeans/_version_check.py | |
misc/_version_check.py | |
modeller/_version_check.py | |
multifit/_version_check.py | |
parallel/_version_check.py | |
pepdock/_version_check.py | |
restrainer/_version_check.py | |
rmf/_version_check.py | |
rotamer/_version_check.py | |
saxs/_version_check.py | |
score_functor/_version_check.py | |
scratch/_version_check.py | |
statistics/_version_check.py | |
system/_version_check.py | |
test/_version_check.py | |
_xml_parser.py | |
AbstractGrid.py | |
add_fit_rmsd.py | |
AddScores.h | A Score on the distance between a pair of particles |
algebra.h | |
algebra_config.h | |
algebra_macros.h | Various important macros for implementing geometry |
align.py | |
align2D.h | Alignment of images in 2D Copyright 2007-2013 IMP Inventors. All rights reserved |
AlignmentParams.h | Parameters for alignments |
AlignSymmetric.h | Fast alignment of a cyclic model to its density |
AllBipartitePairContainer.h | Return all pairs from a SingletonContainer |
AllPairContainer.h | Return all pairs from a SingletonContainer |
AmbiguousNOERestraint.h | A lognormal restraint that uses the ISPA model to model NOE-derived distance fit |
AmbiguousRestraint.h | An implementation of the d-norm to make an ambiguous restraint |
analysis.h | Functions to get report statistics about the used attributes |
Analysis.py | |
analyze_convergence.py | |
anchor_graph.h | Anchor graph utilities |
anchor_utilities.h | Common functions in anchor calculations |
anchors.py | |
anchors_reader.h | Handles reading of anchors data |
angle_decorators.h | Decorators for angles |
AngleRestraint.h | Angle restraint between three particles |
AngleSingletonScore.h | A score on the deviation of an angle from ideality |
AngleTripletScore.h | A Score on the angle between three particles |
argminmax.py | |
Array.h | Classes to handle static sized arrays of things |
assess_dope.py | |
Assignment.h | A beyesian infererence-based sampler |
assignment_containers.h | A beyesian infererence-based sampler |
assignment_tables.h | A beyesian infererence-based sampler |
associations.h | Handle read/write of Model data from/to files |
atom/Atom.h | Simple atom decorator |
Atom.h | |
atom_config.h | |
atom_io.h | Handle read/write of Model data from/to files |
atom_links.h | Handle read/write of Model data from/to files |
atom_macros.h | Various important macros for implementing decorators |
atomicDomino.py | |
atomicDominoUtilities.py | |
AttributeSingletonScore.h | A score based on the unmodified value of an attribute |
BallMover.h | A modifier which variables within a ball |
base.h | |
base_config.h | |
base_macros.h | Various general useful macros for IMP |
base_types.h | Import IMP/kernel/base_types.h in the namespace |
kernel/base_types.h | Basic types used by IMP |
basic_display.py | |
basic_geometry.py | |
basic_optimization.py | |
basic_setup.py | |
benchmark.h | |
benchmark_config.h | |
benchmark_macros.h | Various general useful macros for IMP |
BerendsenThermostatOptimizerState.h | Maintains temperature during molecular dynamics using a Berendsen thermostat |
BildWriter.h | Writer for the Chimera BILD file format |
bipartite_nonbonded_interactions.py | |
bivariate_functions.h | Classes for general functions |
blame.h | Various important functionality for implementing decorators |
bond_decorators.h | Contains decorators for a bond |
bond_graph.h | Contains decorators for a bond |
BondedPairFilter.h | A fake container for bonds |
BondEndpointsRefiner.h | Return the endpoints of a bond |
BondPairContainer.h | A fake container for bonds |
BondSingletonScore.h | A Score on the distance between a the two particles in a bond |
BoundingBox3DSingletonScore.h | Score particles based on a bounding box |
BoundingBoxD.h | A bounding box in D dimensions |
BoxSweepClosePairsFinder.h | Test all pairs of particles to find close pairs |
bracket_macros.h | Various general useful macros for IMP |
BranchAndBoundSampler.h | A beyesian infererence-based sampler |
brownian_statistics.py | |
BrownianDynamics.h | Simple molecular dynamics optimizer |
build.py | |
buildxlinks.py | |
cache.h | Various general useful functions for IMP |
CenteredMat.h | Decorator for OpenCV matrix to use relative coordinates Copyright 2007-2013 IMP Inventors. All rights reserved |
CentroidOfRefined.h | Set the coordinates of the particle to be the centoid of the refined particles |
cg_pdb.py | |
cgal.h | |
cgal_config.h | |
Chain.h | Store the chain ID |
chain.py | |
Charged.h | A decorator for a point particle that has an electrostatic charge |
charmm_forcefield.py | |
charmm_forcefield_verbose.py | |
charmm_segment_topology.h | Classes for handling CHARMM-style topology of segments |
charmm_topology.h | Classes for handling CHARMM-style topology |
CHARMMAtom.h | A decorator for an atom that has a defined CHARMM type |
CHARMMParameters.h | Access to Charmm force field parameters |
CHARMMStereochemistryRestraint.h | Class to maintain CHARMM stereochemistry |
check_macros.h | Exception definitions and assertions |
ChecksScoreState.h | Turn checks on and off |
ChildrenRefiner.h | Return the hierarchy children of a particle |
chimera_models.py | |
ChimeraWriter.h | A writer for Chimera python files |
ChiScore.h | Basic chi score implementation |
ChiScoreLog.h | Scoring with log intensity |
close_pairs_finder_macros.h | Various important macros for implementing decorators |
CloseBipartitePairContainer.h | Return all pairs from a SingletonContainer |
ClosedCubicSpline.h | Closed cubic spline function |
ClosePairContainer.h | Return all pairs from a SingletonContainer |
ClosePairsFinder.h | A base class for algorithms to detect proximities |
ClosePairsPairScore.h | Apply a PairScore to close pairs |
cluster.py | |
cluster_coarse.py | |
clustering_macros.h | Various important macros for implementing decorators |
clustering_of_pdb_models.py | |
CMMWriter.h | A writer for chimera CMM files |
cn_rmsd.h | High-level functions for RMSD calculation |
cnmultifit.h | |
cnmultifit.py | |
cnmultifit_config.h | |
CnSymmAxisDetector.h | Detect cn symmetry in proteins and density maps |
coarse_molecule.h | Coarsen molecule by clustering |
CoarseCC.h | Perform coarse fitting between two density objects |
CoarseCCatIntervals.h | Cross correlation coefficient calculator |
CoarseConvolution.h | Convolutes two grids |
collision_cross_section.py | |
CollisionCrossSection.h | Copyright 2007-2013 IMP Inventors. All rights reserved |
Color.h | Represent a color |
Colored.h | A decorator for a particle with a color |
CommonEndpointPairFilter.h | A fake filter that returns true for any pair of bonds with |
comparison_macros.h | Various general useful macros for IMP |
compat_subprocess.py | |
compatibility.h | |
compiler_macros.h | Various compiler workarounds |
ComplementarityRestraint.h | Calculate weighted excluded volume between rigid bodies |
complex_assembly.h | A simple unary function |
complex_to_anchor_graph.py | |
compute_chi.cpp | |
Cone3D.h | Stores a cone |
Configuration.h | Import IMP/kernel/Configuration.h in the namespace |
kernel/Configuration.h | Store a set of configurations of the model |
ConfigurationSet.h | Import IMP/kernel/ConfigurationSet.h in the namespace |
kernel/ConfigurationSet.h | Store a set of configurations of the model |
core/ConjugateGradients.h | Simple conjugate gradients optimizer |
gsl/ConjugateGradients.h | A conjugate gradients optimizer from GSL |
ConnectingPairContainer.h | A container which has pairs which ensure a set is connected |
connectivity.py | |
connectivity_restraint.py | |
ConnectivityRestraint.h | Connectivity restraint |
connolly_surface.h | Generate surface for a set of atoms |
ConsecutivePairContainer.h | Return all pairs from a SingletonContainer |
ConstantRestraint.h | Constant restraint |
algebra/constants.h | Various useful constants |
atom/constants.h | Define the elements used in IMP |
constants.h | Import IMP/kernel/constants.h in the namespace |
kernel/constants.h | Various useful constants |
Constraint.h | Import IMP/kernel/Constraint.h in the namespace |
kernel/Constraint.h | A base class for constraints |
ConstVector.h | A beyesian infererence-based sampler |
container.h | |
container_base.h | Import IMP/kernel/container_base.h in the namespace |
kernel/container_base.h | Abstract base class for containers of particles |
container_config.h | |
container_macros.h | Import IMP/kernel/container_macros.h in the namespace |
kernel/container_macros.h | Macros to define containers of objects |
convert_spider_to_jpg.py | |
converters.h | Converters of density values |
Copy.h | A particle with a user-defined type |
core.h | |
core_config.h | |
core_macros.h | Various important macros for implementing decorators |
Cosine.h | Cosine function |
CoulombPairScore.h | Coulomb (electrostatic) score between a pair of particles |
counting.h | A simple unary function |
cover_particles.py | |
CoverBond.h | Cover a bond with a sphere |
CoverRefined.h | Cover a bond with a sphere |
CreateLogContext.h | Logging and error reporting support |
creating_restraints.h | A simple unary function |
csv_related.py | |
cube.py | |
custom_filter.py | |
custom_hierarchy.py | |
CustomXYZR.h | Decorator for a sphere-like particle |
Cylinder3D.h | Stores a cylinder |
Database.py | |
DataObject.h | A modifier which variables within a ball |
DataPointsAssignment.h | Tools for data points assignment, after anchor point segmentation |
decay.py | |
DecayPairContainerOptimizerState.h | Track the particles pairs passed to the pair score |
declare_Geometry.h | Implement geometry for the basic shapes from IMP.algebra |
declare_Model.h | Import IMP/kernel/declare_Model.h in the namespace |
kernel/declare_Model.h | Storage of a model, its restraints, constraints and particles |
declare_Object.h | A shared base class to help in debugging and things |
declare_PairContainer.h | Import IMP/kernel/declare_PairContainer.h in the namespace |
kernel/declare_PairContainer.h | A container for Pairs |
declare_Particle.h | Import IMP/kernel/declare_Particle.h in the namespace |
kernel/declare_Particle.h | Classes to handle individual model particles |
declare_QuadContainer.h | Import IMP/kernel/declare_QuadContainer.h in the namespace |
kernel/declare_QuadContainer.h | A container for Quads |
declare_Restraint.h | Import IMP/kernel/declare_Restraint.h in the namespace |
kernel/declare_Restraint.h | Abstract base class for all restraints |
declare_RestraintSet.h | Import IMP/kernel/declare_RestraintSet.h in the namespace |
kernel/declare_RestraintSet.h | Used to hold a set of related restraints |
declare_ScoringFunction.h | Import IMP/kernel/declare_ScoringFunction.h in the namespace |
kernel/declare_ScoringFunction.h | Storage of a model, its restraints, constraints and particles |
declare_SingletonContainer.h | Import IMP/kernel/declare_SingletonContainer.h in the namespace |
kernel/declare_SingletonContainer.h | A container for Singletons |
declare_TripletContainer.h | Import IMP/kernel/declare_TripletContainer.h in the namespace |
kernel/declare_TripletContainer.h | A container for Triplets |
Decorator.h | Import IMP/kernel/Decorator.h in the namespace |
kernel/Decorator.h | The base class for decorators |
decorator_macros.h | Import IMP/kernel/decorator_macros.h in the namespace |
kernel/decorator_macros.h | Various general useful macros for IMP |
def.h | Definitions for EMBED |
density_analysis.h | Density analysis tools, such as histogram and segmentation |
density_map_volumetrics.h | Classes and functions to handle volumetric properties in Density maps |
density_utilities.h | Density map manipulations |
density_utils.h | Density utilities |
DensityDataPoints.h | Handling of data for anchor points segmentation |
DensityFillingRestraint.h | Score how well the particles fill the density |
DensityHeader.h | Metadata for a density file |
DensityMap.h | Class for handling density maps |
cnmultifit_tools/dependencies.py | |
em_tools/dependencies.py | |
EMageFit/dependencies.py | |
example_app/dependencies.py | |
foxs/dependencies.py | |
integrative_docking/dependencies.py | |
ligand_score/dependencies.py | |
multifit_tools/dependencies.py | |
pdb_tools/dependencies.py | |
rmf_tools/dependencies.py | |
saxs_merge/dependencies.py | |
saxs_tools/dependencies.py | |
dependency_graph.h | Import IMP/kernel/dependency_graph.h in the namespace |
kernel/dependency_graph.h | Build dependency graphs on models |
dependency_graph.py | |
DependencyScoreState.h | A beyesian infererence-based sampler |
deprecation.h | Control display of deprecation information |
deprecation_macros.h | Control display of deprecation information |
DerivativeAccumulator.h | Import IMP/kernel/DerivativeAccumulator.h in the namespace |
kernel/DerivativeAccumulator.h | Class for adding derivatives from restraints to the model |
DerivativeCalculator.h | A class for computing SAXS derivatives |
DerivativesFromRefined.h | Accumulate the derivatives of the refined particles |
DerivativesToRefined.h | Accumulate the derivatives of the refined particles |
DiameterRestraint.h | A restraint to maintain the diameter of a set of points |
Diffusion.h | A decorator for a diffusing particle |
DihedralRestraint.h | Dihedral restraint between four particles |
dihedrals.h | Helpers to extract dihedral information |
DihedralSingletonScore.h | A score on a dihedral angle |
DiscreteSampler.h | A beyesian infererence-based sampler |
display.h | |
display_config.h | |
display_log.py | |
display_macros.h | Macros for display classes |
displaying_ensembles.py | |
distance.h | Distance metrics |
distance_pair_score_macros.h | Various important macros for implementing decorators |
core/DistancePairScore.h | A Score on the distance between a pair of particles |
score_functor/DistancePairScore.h | A Score on the distance between a pair of particles |
DistanceRestraint.h | Distance restraint between two particles |
DistanceToSingletonScore.h | A Score on the distance to a fixed point |
DistributePairsScoreState.h | Apply a PairScore to each Pair in a list |
DistributeQuadsScoreState.h | Apply a QuadScore to each Quad in a list |
DistributeSingletonsScoreState.h | Apply a SingletonScore to each Singleton in a list |
DistributeTripletsScoreState.h | Apply a TripletScore to each Triplet in a list |
Distribution.h | Computes distribution functions |
dock_with_crosslinks.py | |
Domain.h | A decorator for associating an atom::Hierarchy piece with a domain |
domino.h | |
domino_approach.py | |
domino_config.h | |
domino_filter_tables.h | Managing of projection overlap filter |
domino_filters.h | SubsetFilter for checking overlap between projections and images |
domino_macros.h | Various important macros for implementing decorators |
domino_particle_states.h | Particles states for a rigid body that is going to be projected |
DominoModel.py | |
DominoSampler.h | A beyesian infererence-based sampler |
Dope.h | A Score on the distance between a pair of particles |
dope_and_excluded_volume.cpp | |
DopePairScore.h | Dope scoring |
doxygen.h | Import IMP/kernel/doxygen.h in the namespace |
kernel/doxygen.h | Import kernel classes into the IMP scope in docs |
doxygen_macros.h | Various general useful macros for IMP |
DummyRestraint.h | Copyright 2007-2013 IMP Inventors. All rights reserved |
DynamicListPairContainer.h | Store a list of ParticlePairsTemp |
DynamicListQuadContainer.h | Store a list of ParticleQuadsTemp |
DynamicListSingletonContainer.h | Store a list of ParticlesTemp |
DynamicListTripletContainer.h | Store a list of ParticleTripletsTemp |
eigen_analysis.h | Principal component analysis of a set of points |
element.h | Define the elements used in IMP |
Ellipsoid3D.h | Simple 3D ellipsoid class |
em.h | |
em2d.h | |
em2d_config.h | |
Em2DRestraint.h | A restraint to score the fitness of a model to a set of EM images |
em_config.h | |
em_images_conversion.py | |
em_restraint.py | |
emagefit.py | |
emagefit_cluster.py | |
emagefit_dock.py | |
emagefit_score.py | |
em/embedding.h | Cluster sets of points |
statistics/embedding.h | Cluster sets of points |
embedding_macros.h | Various important macros for implementing decorators |
embeddings.h | Cluster sets of points |
EMReaderWriter.h | Classes to read or write density files in EM format |
endian.h | Functions to deal with endian of EM images |
ensemble_analysis.h | |
Entry.py | |
enums.h | Basic types used by IMP |
envelope_penetration.h | Functions for calculation envelope penetration |
EnvelopeFitRestraint.h | Score envelope fit based on map distance transform |
EnvelopePenetrationRestraint.h | Score how well a protein is inside its density |
EnvelopeScore.h | Class for envelope based scoring using MapDistanceTransform |
estimate_threshold_from_molecular_mass.py | |
estimates.h | Estimates of various physical quantities |
EventPairsOptimizerState.h | Define some predicates |
EventQuadsOptimizerState.h | Define some predicates |
EventSingletonsOptimizerState.h | Define some predicates |
EventTripletsOptimizerState.h | Define some predicates |
example.h | |
example_config.h | |
ExampleComplexRestraint.h | A restraint to maintain the diameter of a set of points |
ExampleConstraint.h | A restraint on a list of particle pairs |
ExampleDecorator.h | Add a name to a particle |
ExamplePairScore.h | A Score on the distance between a pair of particles |
ExampleRefCounted.h | An example showing how to make a simple ref counted object |
ExampleRestraint.h | A restraint on a list of particle pairs |
ExampleSingletonModifier.h | A singleton modifier which wraps an attribute into a given range |
ExampleSubsetFilterTable.h | A Score on the distance between a pair of particles |
ExampleTemplateClass.h | Show how to manage a template class with python |
ExampleUnaryFunction.h | A simple unary function |
base/exception.h | Exception definitions and assertions |
exception.h | Import IMP/kernel/exception.h in the namespace |
kernel/exception.h | For backwards compatibility |
excluded_volume.py | |
ExcludedVolumeRestraint.h | A prevent spheres from inter-penetrating |
exp.h | An approximation of the exponential function |
fft_based_rigid_fitting.h | FFT based fitting |
FFToperations.h | Operations involving FFT Copyright 2007-2013 IMP Inventors. All rights reserved |
fifobased_loader.py | |
FIFOBasedGrid.py | |
base/file.h | Handling of file input/output |
file.h | Import IMP/kernel/file.h in the namespace |
kernel/file.h | For backwards compatibility |
filebased_loader.py | |
FileBasedGrid.py | |
filenames_manipulation.h | Generation of projections using the central section theorem Copyright 2007-2013 IMP Inventors. All rights reserved |
filter_close_pairs.py | |
FilterGeometry.h | Implement FilterGeometry |
Fine2DRegistrationRestraint.h | Alignment of 2D projections of a 3D volume Copyright 2007-2013 IMP Inventors. All rights reserved |
fit_fft.py | |
fit_restraint.py | |
FitParameters.h | Copyright 2007-2013 IMP Inventors. All rights reserved |
FitRestraint.h | Calculate score based on fit to EM map |
fitting_clustering.h | Cluster fitting solutions by rmsd |
fitting_solutions_reader_writer.h | Handles reading and writing MultiFit fitting solutions file |
fitting_states.h | Fitting states |
fitting_tools.h | Tools for handling fitting records |
fitting_utils.h | Fitting utilities |
FittingSolutionRecord.h | Stored a multifit fitting solution |
FixedRefiner.h | A particle refiner which returns a fixed set of particles |
flags.h | Various general useful macros for IMP |
FloatIndex.h | Import IMP/kernel/FloatIndex.h in the namespace |
kernel/FloatIndex.h | Various general useful functions for IMP |
FNormal.h | Normal distribution of Function |
force_fields.h | Define functions to add bonds and radii to atoms |
ForceFieldParameters.h | Force field base class |
FormFactorTable.h | A class for computation of atomic and residue level form factors for SAXS calculations |
foxs.cpp | |
Fragment.h | A decorator for associating a Hierachy piece |
frames.h | Handle read/write of Model data from/to files |
functor.h | Import IMP/kernel/functor.h in the namespace |
kernel/functor.h | Various important functionality for implementing decorators |
GaussianProcessInterpolation.h | Normal distribution of Function |
GaussianProcessInterpolationRestraint.h | Restraint and ScoreState for GaussianProcessInterpolation |
GaussianProcessInterpolationRestraintSparse.h | Normal distribution of Function |
GaussianProcessInterpolationSparse.h | Normal distribution of Function |
GaussianRestraint.h | A lognormal restraint that uses the ISPA model to model NOE-derived distance fit |
generate_density_map_of_fixed_dimension.py | |
container/generic.h | Various important functionality for implementing decorators |
core/generic.h | Various important functionality for implementing decorators |
generic.h | Import IMP/kernel/generic.h in the namespace |
kernel/generic.h | Various important functionality for implementing decorators |
geometric_alignment.h | Align sets of points |
geometric_primitive_macros.h | Various important macros for implementing geometry |
GeometricHash.h | Geometric Hashing class |
GeometricPrimitiveD.h | Basic types used by IMP |
geometry.h | Backwards compatibility header |
algebra/geometry.py | |
rmf/geometry.py | |
geometry_io.h | Handle read/write of Model data from/to files |
geometry_macros.h | Macros for display classes |
GeometryProcessor.h | Implement GeometryProcessor |
GeometrySet.h | Implement geometry for the basic shapes from IMP.algebra |
graph.py | |
graph_macros.h | Various general useful macros for IMP |
grid_embeddings.h | A class to represent a voxel grid |
grid_indexes.h | A class to represent a voxel grid |
grid_ranges.h | A class to represent a voxel grid |
grid_space.py | |
grid_storages.h | A class to represent a voxel grid |
grid_utility.h | A class to represent a voxel grid |
GridClosePairsFinder.h | Use a hierarchy of grids to find close pairs |
GridD.h | A class to represent a voxel grid |
gsl.h | |
gsl_config.h | |
GSLOptimizer.h | A base class for GSL-based optimizers |
core/Harmonic.h | Harmonic function |
score_functor/Harmonic.h | A Score on the distance between a pair of particles |
core/HarmonicLowerBound.h | Harmonic lower bound function |
score_functor/HarmonicLowerBound.h | A Score on the distance between a pair of particles |
core/HarmonicUpperBound.h | Harmonic upper bound function |
score_functor/HarmonicUpperBound.h | A Score on the distance between a pair of particles |
HarmonicWell.h | Harmonic function |
hash.h | IO support |
hash_macros.h | Various general useful macros for IMP |
header_converters.h | Functions to convert between ImageHeader and DensityHeader Copyright 2007-2013 IMP Inventors. All rights reserved |
hierarchical_clustering.h | Agglomerative clustering algorithm |
atom/Hierarchy.h | Decorator for helping deal with a hierarchy of molecules |
core/Hierarchy.h | Decorator for helping deal with a hierarchy |
hierarchy_tools.h | A set of useful functionality on IMP::atom::Hierarchy decorators |
Histogram.h | Holds a histogram |
HistogramD.h | Holds a histogram |
History.py | |
hosts.py | |
HybridMonteCarlo.h | A hybrid monte carlo implementation |
idock.py | |
Image.h | IMP images for Electron Microscopy using openCV matrices Copyright 2007-2013 IMP Inventors. All rights reserved |
image_processing.h | Image processing functions |
ImageHeader.h | Header for EM images. Compatible with Spider and Xmipp formats Copyright 2007-2013 IMP Inventors. All rights reserved |
ImageReaderWriter.h | Virtual class for reader/writers of images Copyright 2007-2013 IMP Inventors. All rights reserved |
IMP.h | |
imp_example_app.cpp | |
imp_restraints_in_modeller.py | |
ImproperSingletonScore.h | A score on the deviation of an improper angle from ideality |
InContainerPairFilter.h | A filter for Pairs |
InContainerQuadFilter.h | A filter for Quads |
InContainerSingletonFilter.h | A filter for Singletons |
InContainerTripletFilter.h | A filter for Triplets |
incremental_mc.py | |
IncrementalScoringFunction.h | Simple Monte Carlo optimizer |
Index.h | Basic types used by IMP |
indexes.py | |
input_output.h | Import IMP/kernel/input_output.h in the namespace |
kernel/input_output.h | Single variable function |
input_output_macros.h | Import IMP/kernel/input_output_macros.h in the namespace |
kernel/input_output_macros.h | Macros for inputs and outputs |
InputAdaptor.h | Basic types used by IMP |
interactive.h | Functions to get report statistics about the used attributes |
interactive.py | |
interactive_with_containers.py | |
algebra/io.h | Classes to write entities in algebra to files |
io.h | Import IMP/kernel/io.h in the namespace |
kernel/io.h | Handle read/write of Model data from/to files |
isd.h | |
isd_config.h | |
ISDRestraint.h | A lognormal restraint that uses the ISPA model to model NOE-derived distance fit |
JeffreysRestraint.h | A restraint on a scale parameter |
JPGImageReaderWriter.h | Management of JPG format for EM images Copyright 2007-2013 IMP Inventors. All rights reserved |
kernel.h | |
kernel_config.h | |
KernelParameters.h | Calculates and stores gaussian kernel parameters |
kernel/Key.h | Keys to cache lookup of attribute strings |
Key.h | Import IMP/kernel/Key.h in the namespace |
kernel/key_macros.h | Various general useful macros for IMP |
key_macros.h | Import IMP/kernel/key_macros.h in the namespace |
kmeans/KMeans.h | Interface to k-means open source library (stored internally) |
KMeans.h | |
kmeans.py | |
kmeans_config.h | |
kmeans_example.py | |
LangevinThermostatOptimizerState.h | Maintains temperature during molecular dynamics using a Langevin thermostat |
LeavesRefiner.h | Return the hierarchy children of a particle |
LennardJones.h | A decorator for a particle that has a Lennard-Jones potential well |
LennardJonesPairScore.h | Lennard-Jones score between a pair of particles |
ligand_score.cpp | A class for reading mol2 files |
Linear.h | A linear function |
LinearFit.h | Linear fit of data points |
LinearLowerBound.h | A Score on the distance between a pair of particles |
link.py | |
link_macros.h | Macros for display classes |
links.h | Handle read/write of Model data from/to files |
ListPairContainer.h | Store a list of ParticlePairsTemp |
ListQuadContainer.h | Store a list of ParticleQuadsTemp |
ListSingletonContainer.h | Store a list of ParticlesTemp |
ListTripletContainer.h | Store a list of ParticleTripletsTemp |
live_objects.h | A shared base class to help in debugging and things |
load_modeller_model.py | |
load_protein_restrain_bonds.py | |
local_distance.py | |
local_fitting.py | |
base/log.h | Logging and error reporting support |
kernel/log.h | For backwards compatibility |
log.h | Import IMP/kernel/log.h in the namespace |
log.py | |
log_macros.h | Logging and error reporting support |
logfile.py | |
LogicalORRestraint.h | A lognormal restraint that uses the ISPA model to model NOE-derived distance fit |
LognormalRestraint.h | A lognormal restraint that uses the ISPA model to model NOE-derived distance fit |
LogOptimizerState.h | Write geometry to a file during optimization |
LogPairScore.h | Track the particles pairs passed to the pair score |
LowestRefinedPairScore.h | Score on the lowest scoring pair of the refined pairs |
kernel/macros.h | Various general useful macros for IMP |
macros.h | Import IMP/kernel/macros.h in the namespace |
MaintainScaleOrderConstraint.h | Constrain scales to be ordered and positive |
map.h | Declare an efficient stl-compatible map |
map2pca.py | |
MapDistanceTransform.h | Class for computing a distance transform of the density map |
MapReaderWriter.h | An abstract class for reading a map |
MarginalHBondRestraint.h | A lognormal restraint that uses the ISPA model to model HBond-derived distance fit |
MarginalNOERestraint.h | A lognormal restraint that uses the ISPA model to model NOE-derived distance fit |
marina_party.py | |
markers.py | |
masking.h | Masking tools |
Mass.h | A decorator for particles with mass |
master_communicator.py | |
math.h | Declare an efficient stl-compatible map |
MCCGSampler.h | A Monte Carlo/Conjugate Gradients based sampler |
doc/examples/domino/merge_tree.py | |
lib/IMP/multifit/merge_tree.py | |
merge_tree_utils.h | |
Metric.h | Cluster sets of points |
metric_clustering.h | Cluster sets of points |
metric_macros.h | Various important macros for implementing decorators |
metrics.h | Cluster sets of points |
MinimumPairRestraint.h | Score based on the minimum score over a set of Pairs |
MinimumPairScore.h | Define PairScore |
MinimumQuadRestraint.h | Score based on the minimum score over a set of Quads |
MinimumQuadScore.h | Define QuadScore |
MinimumRestraint.h | Score based on the k minimum restraints |
MinimumSingletonRestraint.h | Score based on the minimum score over a set of Singletons |
MinimumSingletonScore.h | Define SingletonScore |
MinimumTripletRestraint.h | Score based on the minimum score over a set of Triplets |
MinimumTripletScore.h | Define TripletScore |
misc.h | |
misc_config.h | |
kernel/Model.h | Storage of a model, its restraints, constraints and particles |
Model.h | Import IMP/kernel/Model.h in the namespace |
model_interaction.h | Operations implying interaction of models and the EM module |
model_statistics.h | Log the restraint scores and things |
modeller.h | |
modeller_config.h | |
modeller_restraints_in_imp.py | |
kernel/ModelObject.h | Single variable function |
ModelObject.h | Import IMP/kernel/ModelObject.h in the namespace |
models.py | |
mol2.h | Functions to read mol2s |
mol2pca.py | |
MolCnSymmAxisDetector.h | Molecule symmetry detector |
molecular_hierarchy.py | |
atom/MolecularDynamics.h | Simple molecular dynamics optimizer |
isd/MolecularDynamics.h | Simple molecular dynamics optimizer |
MolecularDynamicsMover.h | A modifier which perturbs XYZs or Nuisances with a constant energy MD simulation |
Molecule.h | A decorator for Molecules |
monte_carlo_macros.h | Various important macros for implementing decorators |
MonteCarlo.h | Simple Monte Carlo optimizer |
MonteCarloMover.h | The base class for movers for MC optimization |
MonteCarloRelativeMoves.py | |
Mover.h | Backwards compatibility |
mover_macros.h | Backwards compatibility |
MoverBase.h | Backwards compatibility |
MoveStatisticsScoreState.h | Write geometry to a file during optimization |
MRCReaderWriter.h | Classes to read or write MRC files |
ms_connectivity_restraint.py | |
MSConnectivityRestraint.h | Mass Spec Connectivity restraint |
multifit.h | |
multifit.py | |
multifit_config.h | |
MultipleBinormalRestraint.h | Modeller-style multiple binormal (phi/psi) restraint |
multiresolution.py | |
multiscale.py | |
MultivariateFNormalSufficient.h | Normal distribution of Function |
MultivariateFNormalSufficientSparse.h | Normal distribution of Function |
NearestNeighborsClosePairsFinder.h | Test all pairs of particles to find close pairs |
NOERestraint.h | A lognormal restraint that uses the ISPA model to model NOE-derived distance fit |
nonbonded_interactions.py | |
NonCopyable.h | Basic types used by IMP |
NormalMover.h | A modifier which perturbs a point with a normal distribution |
Nuisance.h | A decorator for nuisance parameters particles |
NuisanceRangeModifier.h | A singleton modifier which wraps an attribute into a given range |
nullptr.h | Provide a nullptr keyword analog |
nullptr_macros.h | Provide a nullptr keyword analog |
nup84.py | |
nup84_complex_in_bead_representation.py | |
base/Object.h | A shared base class to help in debugging and things |
kernel/Object.h | A shared base class to help in debugging and things |
Object.h | Import IMP/kernel/Object.h in the namespace |
object_cast.h | A shared base class to help in debugging and things |
object_macros.h | Various general useful macros for IMP |
core/OpenCubicSpline.h | Open cubic spline function |
score_functor/OpenCubicSpline.h | A Score on the distance between a pair of particles |
opencv_interface.h | Inteface with OpenCV Copyright 2007-2013 IMP Inventors. All rights reserved |
optimize_balls.py | |
optimize_em2d_with_montecarlo.py | |
kernel/Optimizer.h | Base class for all optimizers |
Optimizer.h | Import IMP/kernel/Optimizer.h in the namespace |
kernel/optimizer_macros.h | Various general useful macros for IMP |
optimizer_macros.h | Import IMP/kernel/optimizer_macros.h in the namespace |
kernel/optimizer_state_macros.h | Various general useful macros for IMP |
optimizer_state_macros.h | Import IMP/kernel/optimizer_state_macros.h in the namespace |
kernel/OptimizerState.h | Shared optimizer state |
OptimizerState.h | Import IMP/kernel/OptimizerState.h in the namespace |
optimizing.h | A simple unary function |
Order.h | A beyesian infererence-based sampler |
OrderedDict.py | |
osPeptideDocker.py | |
kernel/pair_macros.h | Macros for various classes |
pair_macros.h | Import IMP/kernel/pair_macros.h in the namespace |
pair_predicates.h | Define some predicates |
pair_restraint.py | |
PairConstraint.h | Use a PairModifier applied to a ParticlePairsTemp to maintain an invariant |
kernel/PairContainer.h | A container for Pairs |
PairContainer.h | Import IMP/kernel/PairContainer.h in the namespace |
PairContainerSet.h | Store a set of PairContainers |
PairContainerStatistics.h | A container for Pairs |
kernel/PairDerivativeModifier.h | A Modifier on ParticlePairsTemp |
PairDerivativeModifier.h | Import IMP/kernel/PairDerivativeModifier.h in the namespace |
kernel/PairModifier.h | A Modifier on ParticlePairsTemp |
PairModifier.h | Import IMP/kernel/PairModifier.h in the namespace |
kernel/PairPredicate.h | Define PairPredicate |
PairPredicate.h | Import IMP/kernel/PairPredicate.h in the namespace |
PairRestraint.h | Apply a PairScore to a Pair |
PairsConstraint.h | Use a PairModifier applied to a ParticlePairsTemp to maintain an invariant |
kernel/PairScore.h | Define PairScore |
PairScore.h | Import IMP/kernel/PairScore.h in the namespace |
PairsOptimizerState.h | Use a PairModifier applied to a ParticlePairsTemp to maintain an invariant |
PairsRestraint.h | Apply a PairScore to each Pair in a list |
ParabolicFit.h | Fit the data with parabola |
parallel.h | |
parallel_config.h | |
cnmultifit/param.py | |
multifit/param.py | |
kernel/Particle.h | Classes to handle individual model particles |
Particle.h | Import IMP/kernel/Particle.h in the namespace |
particle_geometry.h | Represent an XYZR particle with a sphere |
kernel/particle_index.h | Various general useful functions for IMP |
particle_index.h | Import IMP/kernel/particle_index.h in the namespace |
particle_io.h | Handle read/write of Model data from/to files |
particle_states.h | A beyesian infererence-based sampler |
kernel/ParticleTuple.h | Classes to handle individual model particles |
ParticleTuple.h | Import IMP/kernel/ParticleTuple.h in the namespace |
partitional_clustering_macros.h | Various important macros for implementing decorators |
PartitionalClustering.h | Compute a distance metric between two points |
PartitionalClusteringWithCenter.h | Cluster sets of points |
path_reader_writer.h | Read and write paths |
pca_based_rigid_fitting.h | Preforms rigid fitting between a set of particles and a density map |
PCAAligner.h | Copyright 2007-2013 IMP Inventors. All rights reserved |
PCAFitRestraint.h | Calculate match between density map PCA and particles PCA |
pdb.h | Functions to read pdbs |
pdb.py | |
pdb2density.py | |
pdb_check.cpp | |
pdb_rmf.cpp | |
pepdock.h | |
pepdock_config.h | |
peptideDocker.py | |
periodic_optimizer_state_macros.h | Various important macros for implementing decorators |
PeriodicOptimizerState.h | Angle restraint between three particles |
piecewise_linear_distribution.h | Boost piecewise linear |
Plane3D.h | Simple 3D plane class |
point_clustering.h | Cluster sets of points |
base/Pointer.h | A nullptr-initialized pointer to an IMP Object |
kernel/Pointer.h | For backwards compatibility |
Pointer.h | Import IMP/kernel/Pointer.h in the namespace |
PolarResamplingParameters.h | Funtions related with rotations in em2d Copyright 2007-2013 IMP Inventors. All rights reserved |
PredicatePairsRestraint.h | Apply a PairScore to each Pair in a list |
PredicateQuadsRestraint.h | Apply a QuadScore to each Quad in a list |
predicates.h | Score particles based on a bounding box |
PredicateSingletonsRestraint.h | Apply a SingletonScore to each Singleton in a list |
PredicateTripletsRestraint.h | Apply a TripletScore to each Triplet in a list |
primitive_geometries.h | Implement geometry for the basic shapes from IMP.algebra |
Profile.h | A class for profile storing and computation |
profile.py | |
profile_fit.py | |
ProfileFitter.h | Class for fitting two profiles |
Profiler.h | Various utilities for benchmarking |
project.h | Generation of projections from models or density maps Copyright 2007-2013 IMP Inventors. All rights reserved |
ProjectionFinder.h | Coarse registration of 2D projections from a 3D volume |
ProjectionMask.h | Projection masks Copyright 2007-2013 IMP Inventors. All rights reserved |
ProjectionParameters.h | Decorator for projection parameters Copyright 2007-2013 IMP Inventors. All rights reserved |
protein_anchors_mapping_reader.h | Handles reading matches between a protein and its anchors |
protein_ligand_score.h | Functions to read mol2s |
proteomics.py | |
proteomics_em_alignment_atomic.h | Align proteomics graph to em density map |
proteomics_reader.h | Handles reading of proteomics data |
PymolWriter.h | Implement PymolWriter |
PyroGrid.py | |
PyroHandlerLoader.py | |
PyroUtils.py | |
algebra/python_only.h | Functionality only availble in python |
atom/python_only.h | Functionality only availble in python |
core/python_only.h | Functionality only availble in python |
display/python_only.h | Build dependency graphs on models |
kernel/python_only.h | Build dependency graphs on models |
python_only.h | Import IMP/kernel/python_only.h in the namespace |
statistics/python_only.h | Python-only functionality |
kernel/quad_macros.h | Macros for various classes |
quad_macros.h | Import IMP/kernel/quad_macros.h in the namespace |
quad_predicates.h | Define some predicates |
QuadConstraint.h | Use a QuadModifier applied to a ParticleQuadsTemp to maintain an invariant |
kernel/QuadContainer.h | A container for Quads |
QuadContainer.h | Import IMP/kernel/QuadContainer.h in the namespace |
QuadContainerSet.h | Store a set of QuadContainers |
QuadContainerStatistics.h | A container for Quads |
kernel/QuadDerivativeModifier.h | A Modifier on ParticleQuadsTemp |
QuadDerivativeModifier.h | Import IMP/kernel/QuadDerivativeModifier.h in the namespace |
kernel/QuadModifier.h | A Modifier on ParticleQuadsTemp |
QuadModifier.h | Import IMP/kernel/QuadModifier.h in the namespace |
kernel/QuadPredicate.h | Define QuadPredicate |
QuadPredicate.h | Import IMP/kernel/QuadPredicate.h in the namespace |
QuadraticClosePairsFinder.h | Test all pairs of particles to find close pairs |
QuadRestraint.h | Apply a QuadScore to a Quad |
QuadsConstraint.h | Use a QuadModifier applied to a ParticleQuadsTemp to maintain an invariant |
kernel/QuadScore.h | Define QuadScore |
QuadScore.h | Import IMP/kernel/QuadScore.h in the namespace |
QuadsOptimizerState.h | Use a QuadModifier applied to a ParticleQuadsTemp to maintain an invariant |
QuadsRestraint.h | Apply a QuadScore to each Quad in a list |
QuasiNewton.h | A GSL-based Quasi-Newton optimizer |
multifit/RadiusOfGyrationRestraint.h | Radius of gyration restraint |
saxs/RadiusOfGyrationRestraint.h | Calculate score based on fit to SAXS profile |
RAII.h | Basic types used by IMP |
raii_macros.h | Various general useful macros for IMP |
base/random.h | Random number generators used by IMP |
kernel/random.h | For backwards compatibility |
random.h | Import IMP/kernel/random.h in the namespace |
randomize_rigid_body.py | |
randomizing.h | A simple unary function |
range_restriction.py | |
RecursivePartitionalClusteringEmbedding.h | Cluster sets of points |
RecursivePartitionalClusteringMetric.h | Cluster sets of points |
ref_counted_macros.h | Various general useful macros for IMP |
base/RefCounted.h | A common base class for ref counted objects |
kernel/RefCounted.h | For backwards compatibility |
RefCounted.h | Import IMP/kernel/RefCounted.h in the namespace |
reference.py | |
ReferenceFrame3D.h | Simple 3D rotation class |
refine_fft.py | |
RefinedPairsPairScore.h | Generate pairs by applying a Refiner to the paricles |
kernel/Refiner.h | Refine a particle into a list of particles |
Refiner.h | Import IMP/kernel/Refiner.h in the namespace |
kernel/refiner_macros.h | Various general useful macros for IMP |
refiner_macros.h | Import IMP/kernel/refiner_macros.h in the namespace |
Reflection3D.h | Reflect about a plane in 3D |
RegistrationResult.h | Registration results class Copyright 2007-2013 IMP Inventors. All rights reserved |
RelativePositionMover.h | Mover for Rigid Bodies moving respect to each other |
RemoveRigidMotionOptimizerState.h | Remove rigid rotation and translation during molecular dynamics |
RemoveTranslationOptimizerState.h | Remove rigid translation during optimization |
Replica.py | |
RepulsiveDistancePairScore.h | A simple quadric repulsive term between two atoms. Restraint is zero when the distance equals the sum of the radii plus the shift |
resample_density.py | |
Residue.h | A decorator for Residues |
restrain_diameter.py | |
restrain_in_sphere.py | |
restrain_minimum_distance.py | |
restrainer.h | |
restrainer_config.h | |
kernel/Restraint.h | Abstract base class for all restraints |
Restraint.h | Import IMP/kernel/Restraint.h in the namespace |
saxs/Restraint.h | Calculate score based on fit to SAXS profile |
restraint_cache.py | |
restraint_geometry.h | Represent an XYZR restraint with a sphere |
restraint_io.h | Handle read/write of Model data from/to files |
kernel/restraint_macros.h | Various general useful macros for IMP |
restraint_macros.h | Import IMP/kernel/restraint_macros.h in the namespace |
restraints.py | |
kernel/RestraintSet.h | Used to hold a set of related restraints |
RestraintSet.h | Import IMP/kernel/RestraintSet.h in the namespace |
RestraintsScoringFunction.h | Storage of a model, its restraints, constraints and particles |
rg.cpp | |
rigid_bodies.h | Functionality for defining rigid bodies |
rigid_bodies.py | |
rigid_body_and_excluded_volume_restraint.py | |
rigid_body_excluded_volume.py | |
rigid_body_geometries.h | Functionality for defining rigid bodies |
rigid_brownian_dynamics.py | |
rigid_collisions.py | |
rigid_fitting.h | Preforms rigid fitting between a set of particles and a density map |
RigidBodiesImageFitRestraint.h | Fit Restraint |
RigidBodyDistancePairScore.h | Act on the distance between two rigid bodies |
RigidBodyMover.h | A mover that transform a rigid body |
RigidClosePairsFinder.h | Handle rigid bodies by looking at their members |
rmf.h | |
rmf_color.cpp | |
rmf_config.h | |
rmf_display.cpp | |
RMFWriter.h | Handle read/write of Model data from/to files |
rmsd.py | |
RMSDClustering.h | Cluster transformations by rmsd |
ro.py | |
rotamer.h | |
rotamer_config.h | |
rotamer_pdb.py | |
rotamer_pdb2.py | |
RotamerCalculator.h | Object performing rotations by Chi angles |
RotamerLibrary.h | Object representing rotamer library |
Rotation2D.h | Classes and operations related with rotations |
Rotation3D.h | Simple 3D rotation class |
SameResiduePairFilter.h | A Score on the distance between a pair of particles |
SampledDensityMap.h | Sampled density map |
kernel/Sampler.h | Base class for all samplers |
Sampler.h | Import IMP/kernel/Sampler.h in the namespace |
kernel/sampler_macros.h | Various general useful macros for IMP |
sampler_macros.h | Import IMP/kernel/sampler_macros.h in the namespace |
sampling.py | |
save_assignments.py | |
SaveOptimizerState.h | Handle read/write of Model data from/to files |
saxs.h | |
saxs_config.h | |
saxs_merge.py | |
saxs_restraint.py | |
Scale.h | A decorator for scale parameters particles |
kernel/scoped.h | Various general useful functions for IMP |
scoped.h | Import IMP/kernel/scoped.h in the namespace |
Score.h | A Score on the distance between a pair of particles |
score.py | |
score_functor.h | |
score_functor_config.h | |
score_protein_with_ligand.py | |
kernel/score_state_macros.h | Various general useful macros for IMP |
score_state_macros.h | Import IMP/kernel/score_state_macros.h in the namespace |
kernel/ScoreAccumulator.h | Class for adding scores from restraints to the model |
ScoreAccumulator.h | Import IMP/kernel/ScoreAccumulator.h in the namespace |
scores2D.h | Scoring functions for 2D Copyright 2007-2013 IMP Inventors. All rights reserved |
kernel/ScoreState.h | Shared score state |
ScoreState.h | Import IMP/kernel/ScoreState.h in the namespace |
ScoreUnaryFunction.h | A Score on the distance between a pair of particles |
kernel/scoring_function_macros.h | Various general useful macros for IMP |
scoring_function_macros.h | Import IMP/kernel/scoring_function_macros.h in the namespace |
kernel/ScoringFunction.h | Storage of a model, its restraints, constraints and particles |
ScoringFunction.h | Import IMP/kernel/ScoringFunction.h in the namespace |
scratch.h | |
scratch_config.h | |
secondary_structure_reader.h | Functions to read PSIPRED/DSSP and encode as SSES |
SecondaryStructureResidue.h | A decorator for storing secondary structure probabilities. Copyright 2007-2013 IMP Inventors. All rights reserved |
Segment3D.h | Simple implementation of segments in 3D |
Selection.h | A set of useful functionality on IMP::atom::Hierarchy decorators |
SerialMover.h | A mover that apply other movers one at a time |
serialPeptideDocker.py | |
set.h | Declare an efficient stl-compatible set |
SetCheckState.h | Checkging and error reporting support |
SetLogState.h | Logging and error reporting support |
SettingsData.h | Stored multifit settings data |
setup.py | |
shared_functions.py | |
Shift.h | A Score on the distance between a pair of particles |
shortest_segment.h | Predicates implemented using CGAL Copyright 2007-2013 IMP Inventors. All rights reserved |
show_particles_as_spheres.py | |
Showable.h | IO support |
showable_macros.h | Various general useful macros for IMP |
simple_connectivity_on_molecules.py | |
simple_connectivity_on_rigid_bodies.py | |
simple_diameter.py | |
simple_distance.py | |
simple_em_fit.py | |
simple_excluded_volume.py | |
simple_links.h | Handle read/write of Model data from/to files |
Simplex.h | The simplex algorithm from GSL |
simplex.py | |
simplify_restraint.h | Restrainer functions for restraints |
simulate_density_from_pdb.py | |
simulation.py | |
Simulator.h | Simple molecular dynamics optimizer |
kernel/singleton_macros.h | Macros for various classes |
singleton_macros.h | Import IMP/kernel/singleton_macros.h in the namespace |
singleton_predicates.h | Define some predicates |
SingletonConstraint.h | Use a SingletonModifier applied to a ParticlesTemp to maintain an invariant |
kernel/SingletonContainer.h | A container for Singletons |
SingletonContainer.h | Import IMP/kernel/SingletonContainer.h in the namespace |
SingletonContainerSet.h | Store a set of SingletonContainers |
SingletonContainerStatistics.h | A container for Singletons |
kernel/SingletonDerivativeModifier.h | A Modifier on ParticlesTemp |
SingletonDerivativeModifier.h | Import IMP/kernel/SingletonDerivativeModifier.h in the namespace |
kernel/SingletonModifier.h | A Modifier on ParticlesTemp |
SingletonModifier.h | Import IMP/kernel/SingletonModifier.h in the namespace |
kernel/SingletonPredicate.h | Define SingletonPredicate |
SingletonPredicate.h | Import IMP/kernel/SingletonPredicate.h in the namespace |
SingletonRestraint.h | Apply a SingletonScore to a Singleton |
SingletonsConstraint.h | Use a SingletonModifier applied to a ParticlesTemp to maintain an invariant |
kernel/SingletonScore.h | Define SingletonScore |
SingletonScore.h | Import IMP/kernel/SingletonScore.h in the namespace |
SingletonsOptimizerState.h | Use a SingletonModifier applied to a ParticlesTemp to maintain an invariant |
SingletonsRestraint.h | Apply a SingletonScore to each Singleton in a list |
six_particles_optimization.py | |
slave_handler.py | |
slavestate.py | |
Slice.h | A beyesian infererence-based sampler |
SlidingPriorRestraint.h | A restraint on a scale parameter |
smoothing_functions.h | Classes to smooth nonbonded interactions |
SoftCylinderPairScore.h | A Score on the distance between a pair of particles |
solutions_io.py | |
SolventAccessibleSurface.h | Copyright 2007-2013 IMP Inventors. All rights reserved |
Sphere3D.h | Simple 3D sphere class |
SphereD.h | Simple 3D sphere class |
SphereDistance.h | A Score on the distance between a pair of particles |
SphereDistancePairScore.h | A score on the distance between the surfaces of two spheres |
SpherePatch3D.h | Simple 3D sphere patch class |
SphericalVector3D.h | Stores and converts spherical coordinates |
SpiderHeader.h | Header for Spider and Xmipp formats |
SpiderImageReaderWriter.h | Management of Images in Spider format Copyright 2007-2013 IMP Inventors. All rights reserved |
SpiderReaderWriter.h | Management of Spider Headers Electron Microscopy. Compatible with Spider and Xmipp formats Copyright 2007-2013 IMP Inventors. All rights reserved |
standard_grids.h | A class to represent a voxel grid |
StateAdaptor.h | XXXXXXXXXXXXXX |
Statistical.h | A Score on the distance between a pair of particles |
StatisticalPairScore.h | Functions to read mol2s |
statistics.h | |
Statistics.py | |
statistics_config.h | |
SteepestDescent.h | Simple steepest descent optimizer |
StereochemistryPairFilter.h | A filter that excludes bonds, angles and dihedrals |
structure_from_sequence.py | |
subproc.py | |
Subset.h | A beyesian infererence-based sampler |
subset_filters.h | A beyesian infererence-based sampler |
subset_graphs.h | A beyesian infererence-based sampler |
subset_scores.h | A beyesian infererence-based sampler |
surface.py | |
SurfaceShellDensityMap.h | Represent a molecule as shells of distance from the surface |
swap_macros.h | Various general useful macros for IMP |
swig_macros.h | Various general useful macros for IMP |
Switching.h | A decorator for switching parameters particles |
symmetric_multifit.h | Build cyclic symmetric complexes |
symmetry.h | Implement various types of symmetry |
symmetry.py | |
symmetry_utils.h | Symmetry utilities |
system.h | |
system_config.h | |
TableRefiner.h | A lookup based particle refiner |
TALOSReader.py | |
TALOSRestraint.h | TALOS dihedral restraint between four particles |
tasks.py | |
TBLReader.py | |
test.h | |
thread_macros.h | Control for OpenMP |
threads.h | Control for using multiple threads in IMP |
TIFFImageReaderWriter.h | Management of reading/writing TIFF images |
tracking.h | IO support |
Transform.h | Transform a particle |
Transformation2D.h | 2D transformations. Copyright 2007-2013 IMP Inventors. All rights reserved |
Transformation3D.h | Simple 3D transformation class |
TransformationClustering.h | Clustering of transformation |
TransformedDistancePairScore.h | A score on the distance between a pair of particles after transforming one |
transforms.py | |
Triangle3D.h | Simple implementation of a triangle in 3D |
kernel/triplet_macros.h | Macros for various classes |
triplet_macros.h | Import IMP/kernel/triplet_macros.h in the namespace |
triplet_predicates.h | Define some predicates |
TripletConstraint.h | Use a TripletModifier applied to a ParticleTripletsTemp to maintain an invariant |
kernel/TripletContainer.h | A container for Triplets |
TripletContainer.h | Import IMP/kernel/TripletContainer.h in the namespace |
TripletContainerSet.h | Store a set of TripletContainers |
TripletContainerStatistics.h | A container for Triplets |
kernel/TripletDerivativeModifier.h | A Modifier on ParticleTripletsTemp |
TripletDerivativeModifier.h | Import IMP/kernel/TripletDerivativeModifier.h in the namespace |
kernel/TripletModifier.h | A Modifier on ParticleTripletsTemp |
TripletModifier.h | Import IMP/kernel/TripletModifier.h in the namespace |
kernel/TripletPredicate.h | Define TripletPredicate |
TripletPredicate.h | Import IMP/kernel/TripletPredicate.h in the namespace |
TripletRestraint.h | Apply a TripletScore to a Triplet |
TripletsConstraint.h | Use a TripletModifier applied to a ParticleTripletsTemp to maintain an invariant |
kernel/TripletScore.h | Define TripletScore |
TripletScore.h | Import IMP/kernel/TripletScore.h in the namespace |
TripletsOptimizerState.h | Use a TripletModifier applied to a ParticleTripletsTemp to maintain an invariant |
TripletsRestraint.h | Apply a TripletScore to each Triplet in a list |
TruncatedHarmonic.h | Truncated harmonic |
TuneRex.py | |
tuple_macros.h | Various general useful macros for IMP |
Typed.h | A particle with a user-defined type |
TypedPairScore.h | Delegate to another PairScore depending on particle types |
types.h | Basic types used by IMP |
kernel/unary_function_macros.h | Various general useful macros for IMP |
unary_function_macros.h | Import IMP/kernel/unary_function_macros.h in the namespace |
kernel/UnaryFunction.h | Single variable function |
UnaryFunction.h | Import IMP/kernel/UnaryFunction.h in the namespace |
UnaryFunctionEvaluate.h | A Score on the distance between a pair of particles |
kernel/Undecorator.h | The base class for decorators |
Undecorator.h | Import IMP/kernel/Undecorator.h in the namespace |
univariate_functions.h | Classes for general functions |
util.py | |
algebra/utility.h | Functions to deal with very common math operations |
base/utility.h | Various general useful functions for IMP |
benchmark/utility.h | Various utilities for benchmarking |
core/utility.h | Various important functionality for implementing decorators |
domino/utility.h | Functions to get report statistics about the used attributes |
kernel/utility.h | For backwards compatibility |
saxs/utility.h | Functions to deal with very common saxs operations Copyright 2007-2013 IMP Inventors. All rights reserved |
statistics/utility.h | Cluster sets of points |
utility.h | Import IMP/kernel/utility.h in the namespace |
utility.py | |
utility_macros.h | Various general useful macros for IMP |
utils.py | |
validate_profile.cpp | |
Value.h | Basic types used by IMP |
value_macros.h | Various general useful macros for IMP |
Vector.h | A class for storing lists of IMP items |
Vector2D.h | Simple 2D vector class |
Vector3D.h | Simple 3D vector class |
vector_generators.h | Functions to generate vectors |
vector_metrics.h | Functions to generate vectors |
vector_property_map.h | Include the correct headers to get the boost vector_property_map |
vector_search.h | Functions to generate vectors |
VectorD.h | Simple D vector class |
VelocityScalingOptimizerState.h | Maintains temperature during molecular dynamics by velocity scaling |
base/VersionInfo.h | Version and authorship of IMP objects |
kernel/VersionInfo.h | Version and authorship of IMP objects |
VersionInfo.h | Import IMP/kernel/VersionInfo.h in the namespace |
view_density_header.py | |
VolumeRestraint.h | A prevent spheres from inter-penetrating |
vonMises.h | Normal distribution of Function |
vonMisesKappaConjugateRestraint.h | Conjugate prior for \(\kappa\) in the von Mises distribution |
vonMisesKappaJeffreysRestraint.h | Jeffreys prior for \(\kappa\) in the von Mises distribution |
vonMisesSufficient.h | Normal distribution of Function |
Voxel.h | Voxel decorator |
warning_macros.h | Various general useful macros for IMP |
WarningContext.h | Logging and error reporting support |
base/WeakPointer.h | A nullptr-initialized pointer to an Object |
kernel/WeakPointer.h | For backwards compatibility |
WeakPointer.h | Import IMP/kernel/WeakPointer.h in the namespace |
weighted_excluded_volume.h | Handles low resolution weighted excluded volume calculation |
WeightedExcludedVolumeRestraint.h | Calculate weighted excluded volume between rigid bodies |
WeightScore.h | A Score on the distance between a pair of particles |
WormLikeChain.h | Worm-like-chain score for polymer chains |
write_a_metric.py | |
write_a_restraint.py | |
write_an_optimizer_state.py | |
Writer.h | Base class for writing geometry to a file |
writer_macros.h | Macros for display classes |
XplorReaderWriter.h | Classes to read or write density files in XPLOR format |
XYZ.h | Simple xyz decorator |
XYZ_Decorator.py | |
XYZR.h | Decorator for a sphere-like particle |
XYZR_Decorator.py |