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IMP
2.3.0
The Integrative Modeling Platform
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![]() ![]() | Synonym for IMP::kernel |
![]() ![]() ![]() | General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP modules |
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![]() ![]() ![]() ![]() | An axis-aligned bounding box |
![]() ![]() ![]() ![]() | Represent a cone in 3D |
![]() ![]() ![]() ![]() | Represent a point on the Connolly surface |
![]() ![]() ![]() ![]() | Represent a cylinder in 3D |
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![]() ![]() ![]() ![]() | A dense grid of values |
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![]() ![]() ![]() ![]() | Represent an ellipsoid in 3D |
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![]() ![]() ![]() ![]() | An index in an infinite grid on space |
![]() ![]() ![]() ![]() | A simple class for returning XYZ Euler angles |
![]() ![]() ![]() ![]() | A Gaussian distribution in 3D |
![]() ![]() ![]() ![]() | Base class for geometric types |
![]() ![]() ![]() ![]() | A voxel grid in d-dimensional space space |
![]() ![]() ![]() ![]() | Represent a real cell in a grid (one within the bounding box) |
![]() ![]() ![]() ![]() | Calculate line that fits best the input data points (Linear least squares) |
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![]() ![]() ![]() ![]() | Calculate parabola that fits best the input data points |
![]() ![]() ![]() ![]() | Represent a plane in 3D |
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![]() ![]() ![]() ![]() | A reference frame in 3D |
![]() ![]() ![]() ![]() | Reflect about a plane in 3D |
![]() ![]() ![]() ![]() | Stores a 2D rotation matrix |
![]() ![]() ![]() ![]() | 3D rotation class |
![]() ![]() ![]() ![]() | Simple implementation of segments in 3D |
![]() ![]() ![]() ![]() | A sparse grid of values |
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![]() ![]() ![]() ![]() | A sparse, infinite grid of values |
![]() ![]() ![]() ![]() | A sparse, infinite grid of values |
![]() ![]() ![]() ![]() | Represent a sphere in D-dimensions |
![]() ![]() ![]() ![]() | A sphere patch is defined as all points above the plane and on the sphere |
![]() ![]() ![]() ![]() | Class to represent a 3D point in spherical coordinates |
![]() ![]() ![]() ![]() | Simple 2D transformation class |
![]() ![]() ![]() ![]() | Simple 3D transformation class |
![]() ![]() ![]() ![]() | Represent a triangle in 3D |
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![]() ![]() ![]() ![]() | A Cartesian vector in D-dimensions |
![]() ![]() ![]() ![]() | A Cartesian vector in D-dimensions |
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![]() ![]() ![]() | Functionality for loading, creating, manipulating and scoring atomic structures |
![]() ![]() ![]() ![]() | Read all atoms |
![]() ![]() ![]() ![]() | Defines a selector that will pick every ATOM and HETATM record |
![]() ![]() ![]() ![]() | Select atoms which are selected by both selectors |
![]() ![]() ![]() ![]() | A particle that describes an angle between three particles |
![]() ![]() ![]() ![]() | Score the angle based on a UnaryFunction, |
![]() ![]() ![]() ![]() | A decorator for a particle representing an atom |
![]() ![]() ![]() ![]() | Select all non-alternative ATOM records |
![]() ![]() ![]() ![]() | The type of an atom |
![]() ![]() ![]() ![]() | Select all backbone (N,CA,C,O) ATOM records |
![]() ![]() ![]() ![]() | Maintains temperature during molecular dynamics |
![]() ![]() ![]() ![]() | A decorator for wrapping a particle representing a molecular bond |
![]() ![]() ![]() ![]() | A decorator for a particle which has bonds |
![]() ![]() ![]() ![]() | A filter for bonds |
![]() ![]() ![]() ![]() | Return the endpoints of a bond |
![]() ![]() ![]() ![]() | Display a Bond particle as a segment |
![]() ![]() ![]() ![]() | Represent a bond graph as a boost graph |
![]() ![]() ![]() ![]() | A container that returns pairs of the endpoints of the bonds |
![]() ![]() ![]() ![]() | Display an IMP::SingletonContainer of Bond particles as segments |
![]() ![]() ![]() ![]() | Score the bond based on a UnaryFunction, |
![]() ![]() ![]() ![]() | Simple Brownian dynamics simulator |
![]() ![]() ![]() ![]() | Select all CA ATOM records |
![]() ![]() ![]() ![]() | Select all CB ATOM records |
![]() ![]() ![]() ![]() | A particle that is the center of mass of other particles |
![]() ![]() ![]() ![]() | Store info for a chain of a protein |
![]() ![]() ![]() ![]() | Select all ATOM and HETATM records with the given chain ids |
![]() ![]() ![]() ![]() | A decorator for a point particle that has an electrostatic charge |
![]() ![]() ![]() ![]() | A decorator for an atom that has a defined CHARMM type |
![]() ![]() ![]() ![]() | A single atom in a CHARMM topology |
![]() ![]() ![]() ![]() | The end of a bond, angle, dihedral, improper, or internal coordinate |
![]() ![]() ![]() ![]() | The parameters for a CHARMM bond or angle |
![]() ![]() ![]() ![]() | A connection (bond, angle, dihedral) between some number of endpoints |
![]() ![]() ![]() ![]() | The parameters for a CHARMM dihedral or improper |
![]() ![]() ![]() ![]() | The ideal topology of a single residue |
![]() ![]() ![]() ![]() | A geometric relationship between four atoms |
![]() ![]() ![]() ![]() | CHARMM force field parameters |
![]() ![]() ![]() ![]() | A CHARMM patch residue |
![]() ![]() ![]() ![]() | The topology of a single residue in a model |
![]() ![]() ![]() ![]() | Base class for all CHARMM residue-based topology |
![]() ![]() ![]() ![]() | The topology of a single CHARMM segment in a model |
![]() ![]() ![]() ![]() | Enforce CHARMM stereochemistry on the given Hierarchy |
![]() ![]() ![]() ![]() | The topology of a complete CHARMM model |
![]() ![]() ![]() ![]() | A decorator for keeping track of copies of a molecule |
![]() ![]() ![]() ![]() | Coulomb (electrostatic) score between a pair of particles |
![]() ![]() ![]() ![]() | Cover a bond with a sphere |
![]() ![]() ![]() ![]() | Select all C (not CA or CB) ATOM records |
![]() ![]() ![]() ![]() | A decorator for a diffusing particle with a diffusion coefficient |
![]() ![]() ![]() ![]() | A particle that describes a dihedral angle between four particles |
![]() ![]() ![]() ![]() | Score the dihedral angle |
![]() ![]() ![]() ![]() | A decorator to associate a particle with a part of a protein |
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![]() ![]() ![]() ![]() | Ez Potential kernel::Restraint |
![]() ![]() ![]() ![]() | Storage and access to force field |
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![]() ![]() ![]() ![]() | Smooth interaction scores by switching the derivatives (force switch) |
![]() ![]() ![]() ![]() | A decorator to associate a particle with a part of a protein/DNA/RNA |
![]() ![]() ![]() ![]() | Display an IMP::SingletonContainer of IMP::atom::Hierarchy particles as balls |
![]() ![]() ![]() ![]() | The standard decorator for manipulating molecular structures |
![]() ![]() ![]() ![]() | Display an IMP::atom::Hierarchy particle as balls |
![]() ![]() ![]() ![]() | Select all hydrogen ATOM and HETATM records |
![]() ![]() ![]() ![]() | Score the improper dihedral based on a UnaryFunction, |
![]() ![]() ![]() ![]() | Maintains temperature during molecular dynamics |
![]() ![]() ![]() ![]() | A decorator for a particle that has a Lennard-Jones potential well |
![]() ![]() ![]() ![]() | Lennard-Jones score between a pair of particles |
![]() ![]() ![]() ![]() | Add mass to a particle |
![]() ![]() ![]() ![]() | A base class for choosing which Mol2 atoms to read |
![]() ![]() ![]() ![]() | Simple molecular dynamics optimizer |
![]() ![]() ![]() ![]() | A decorator for a molecule |
![]() ![]() ![]() ![]() | Select all ATOM and HETATM records which are not alternatives |
![]() ![]() ![]() ![]() | Defines a selector that will pick only non-hydrogen atoms |
![]() ![]() ![]() ![]() | Select non water and non hydrogen atoms |
![]() ![]() ![]() ![]() | Select all non-water non-alternative ATOM and HETATM records |
![]() ![]() ![]() ![]() | Select atoms which are not selected by a given selector |
![]() ![]() ![]() ![]() | Select all N ATOM records |
![]() ![]() ![]() ![]() | Score a pair of atoms using an orientation-dependent SOAP score |
![]() ![]() ![]() ![]() | Select atoms which are selected by either selector |
![]() ![]() ![]() ![]() | Select which atoms to read from a PDB file |
![]() ![]() ![]() ![]() | Select all P (= phosphate) ATOM records |
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![]() ![]() ![]() ![]() | Score a pair of molecules |
![]() ![]() ![]() ![]() | Removes rigid translation and rotation from the particles |
![]() ![]() ![]() ![]() | Removes rigid translation from the particles |
![]() ![]() ![]() ![]() | A decorator for a representation |
![]() ![]() ![]() ![]() | A decorator for a residue |
![]() ![]() ![]() ![]() | The type for a residue |
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![]() ![]() ![]() ![]() | A decorator for a residue with probability of secondary structure |
![]() ![]() ![]() ![]() | Select hierarchy particles identified by the biological name |
![]() ![]() ![]() ![]() | Display a Selection |
![]() ![]() ![]() ![]() | The base class for simulators |
![]() ![]() ![]() ![]() | Base class for smoothing nonbonded interactions as a function of distance |
![]() ![]() ![]() ![]() | Filter atom pairs for SOAP |
![]() ![]() ![]() ![]() | Associate an integer "state" index with a hierarchy node |
![]() ![]() ![]() ![]() | A filter that excludes bonds, angles and dihedrals |
![]() ![]() ![]() ![]() | Maintains temperature during molecular dynamics by velocity scaling |
![]() ![]() ![]() ![]() | Select all non-water ATOM and HETATM records |
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![]() ![]() ![]() | Low level functionality (logging, error handling, profiling, command line flags etc) that is used by all of IMP |
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![]() ![]() ![]() ![]() | Use this to add an advanced flag to the program |
![]() ![]() ![]() ![]() | A class to store an fixed array of same-typed values |
![]() ![]() ![]() ![]() | Store an array of values of the same type |
![]() ![]() ![]() ![]() | Create a new log context |
![]() ![]() ![]() ![]() | An exception that signifies some event occurred |
![]() ![]() ![]() ![]() | The general base class for IMP exceptions |
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![]() ![]() ![]() ![]() | An exception for a request for an invalid member of a container |
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![]() ![]() ![]() ![]() | A general exception for an internal error in IMP |
![]() ![]() ![]() ![]() | An input/output exception |
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![]() ![]() ![]() ![]() | An exception which is thrown when the kernel::Model has attributes with invalid values |
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![]() ![]() ![]() ![]() | Common base class for heavy weight IMP objects |
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![]() ![]() ![]() ![]() | A smart pointer to a reference counted object |
![]() ![]() ![]() ![]() | A smart pointer to a ref-counted Object that is a class member |
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![]() ![]() ![]() ![]() | A class to change and restore check state |
![]() ![]() ![]() ![]() | A class to change and restore log state |
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![]() ![]() ![]() ![]() | A weak pointer to an Object or RefCountedObject |
![]() ![]() ![]() ![]() | An exception for an invalid usage of IMP |
![]() ![]() ![]() ![]() | Base for a simple primitive-like type |
![]() ![]() ![]() ![]() | An exception for an invalid value being passed to IMP |
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![]() ![]() ![]() ![]() | Version and module information for Objects |
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![]() ![]() ![]() | Support for developing and analyzing benchmarks of IMP code |
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![]() ![]() ![]() | Make CGAL functionality available to IMP |
![]() ![]() ![]() | Generate cyclic atomic structures using cryo-electron microscopy data |
![]() ![]() ![]() ![]() | A class for fast alignment of a cyclic model to its density |
![]() ![]() ![]() ![]() | Detect cn symmetry in proteins and density maps |
![]() ![]() ![]() ![]() | Molecule symmetry detector |
![]() ![]() ![]() | Various classes to hold sets of particles |
![]() ![]() ![]() ![]() | Return all bipartite pairs between two containers |
![]() ![]() ![]() ![]() | Return all unordered pairs of particles taken from the SingletonContainer |
![]() ![]() ![]() ![]() | Return all close ordered pairs of particles taken from the two SingletonContainers |
![]() ![]() ![]() ![]() | Return all close unordered pairs of particles taken from the SingletonContainer |
![]() ![]() ![]() ![]() | A container which keeps a set of pairs that connect a set of spheres |
![]() ![]() ![]() ![]() | A container which contains all consecutive particle pairs from an input list |
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![]() ![]() ![]() ![]() | Distribute contents of one container into several based on predicates |
![]() ![]() ![]() ![]() | Distribute contents of one container into several based on predicates |
![]() ![]() ![]() ![]() | Distribute contents of one container into several based on predicates |
![]() ![]() ![]() ![]() | Distribute contents of one container into several based on predicates |
![]() ![]() ![]() ![]() | Store a kernel::ParticleIndexPairs |
![]() ![]() ![]() ![]() | Store a kernel::ParticleIndexQuads |
![]() ![]() ![]() ![]() | Store a kernel::ParticleIndexes |
![]() ![]() ![]() ![]() | Store a kernel::ParticleIndexTriplets |
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![]() ![]() ![]() ![]() | A filter which returns true if a container containers the Pair |
![]() ![]() ![]() ![]() | A filter which returns true if a container containers the Quad |
![]() ![]() ![]() ![]() | A filter which returns true if a container containers the Singleton |
![]() ![]() ![]() ![]() | A filter which returns true if a container containers the Triplet |
![]() ![]() ![]() ![]() | Store a kernel::ParticleIndexPairs |
![]() ![]() ![]() ![]() | Store a kernel::ParticleIndexQuads |
![]() ![]() ![]() ![]() | Store a kernel::ParticleIndexes |
![]() ![]() ![]() ![]() | Store a kernel::ParticleIndexTriplets |
![]() ![]() ![]() ![]() | Score based on the min or max PairScore over a set |
![]() ![]() ![]() ![]() | Evaluate the min or max n particle_pair scores of the passed set |
![]() ![]() ![]() ![]() | Score based on the min or max QuadScore over a set |
![]() ![]() ![]() ![]() | Evaluate the min or max n particle_quad scores of the passed set |
![]() ![]() ![]() ![]() | Score based on the min or max SingletonScore over a set |
![]() ![]() ![]() ![]() | Evaluate the min or max n particle scores of the passed set |
![]() ![]() ![]() ![]() | Score based on the min or max TripletScore over a set |
![]() ![]() ![]() ![]() | Evaluate the min or max n particle_triplet scores of the passed set |
![]() ![]() ![]() ![]() | Stores a set of PairContainers |
![]() ![]() ![]() ![]() | Track statistics on a PairContainer |
![]() ![]() ![]() ![]() | Apply a PairFunction to a PairContainer to maintain an invariant |
![]() ![]() ![]() ![]() | Apply a PairFunction to a PairContainer to maintain an invariant |
![]() ![]() ![]() ![]() | Applies a PairScore to each Pair in a list |
![]() ![]() ![]() ![]() | Applies a PairScore to each Pair in a list based on a predicate |
![]() ![]() ![]() ![]() | Applies a QuadScore to each Quad in a list based on a predicate |
![]() ![]() ![]() ![]() | Applies a SingletonScore to each Singleton in a list based on a predicate |
![]() ![]() ![]() ![]() | Applies a TripletScore to each Triplet in a list based on a predicate |
![]() ![]() ![]() ![]() | Stores a set of QuadContainers |
![]() ![]() ![]() ![]() | Track statistics on a QuadContainer |
![]() ![]() ![]() ![]() | Apply a QuadFunction to a QuadContainer to maintain an invariant |
![]() ![]() ![]() ![]() | Apply a QuadFunction to a QuadContainer to maintain an invariant |
![]() ![]() ![]() ![]() | Applies a QuadScore to each Quad in a list |
![]() ![]() ![]() ![]() | Stores a set of SingletonContainers |
![]() ![]() ![]() ![]() | Track statistics on a SingletonContainer |
![]() ![]() ![]() ![]() | Apply a SingletonFunction to a SingletonContainer to maintain an invariant |
![]() ![]() ![]() ![]() | Apply a SingletonFunction to a SingletonContainer to maintain an invariant |
![]() ![]() ![]() ![]() | Applies a SingletonScore to each Singleton in a list |
![]() ![]() ![]() ![]() | Stores a set of TripletContainers |
![]() ![]() ![]() ![]() | Track statistics on a TripletContainer |
![]() ![]() ![]() ![]() | Apply a TripletFunction to a TripletContainer to maintain an invariant |
![]() ![]() ![]() ![]() | Apply a TripletFunction to a TripletContainer to maintain an invariant |
![]() ![]() ![]() ![]() | Applies a TripletScore to each Triplet in a list |
![]() ![]() ![]() | Basic functionality that is expected to be used by a wide variety of IMP users |
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![]() ![]() ![]() ![]() | Angle restraint between three particles |
![]() ![]() ![]() ![]() | Apply a function to the angle between three particles |
![]() ![]() ![]() ![]() | Return the value of an int attribute as the predicate value |
![]() ![]() ![]() ![]() | Modify a set of continuous variables by perturbing them within a ball |
![]() ![]() ![]() ![]() | Find all nearby pairs by sweeping the bounding boxes |
![]() ![]() ![]() ![]() | A particle that is the geometric centroid of other particles |
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![]() ![]() ![]() ![]() | Return the hierarchy children of a particle |
![]() ![]() ![]() ![]() | Closed cubic spline function |
![]() ![]() ![]() ![]() | A base class for algorithms to find spatial proximities |
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![]() ![]() ![]() ![]() | Simple conjugate gradients optimizer |
![]() ![]() ![]() ![]() | Ensure that a set of particles remains connected with one another |
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![]() ![]() ![]() ![]() | Return a constant value |
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![]() ![]() ![]() ![]() | Cosine function |
![]() ![]() ![]() ![]() | A particle which covers a set of other particles |
![]() ![]() ![]() ![]() | This class sets the position and radius of each particle to enclose the refined |
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![]() ![]() ![]() ![]() | Accumulate the derivatives of the refined particles |
![]() ![]() ![]() ![]() | Copy the derivatives from a coarse particle to its refined particles |
![]() ![]() ![]() ![]() | Restrain the diameter of a set of points |
![]() ![]() ![]() ![]() | Dihedral restraint between four particles |
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![]() ![]() ![]() ![]() | Distance restraint between two particles |
![]() ![]() ![]() ![]() | Display a segment connecting a pair of particles |
![]() ![]() ![]() ![]() | Display a segment for each pair in a IMP::kernel::PairContainer |
![]() ![]() ![]() ![]() | Prevent a set of particles and rigid bodies from inter-penetrating |
![]() ![]() ![]() ![]() | The refiner can refine any particle by returning a fixed set |
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![]() ![]() ![]() ![]() | Apply a function to an attribute |
![]() ![]() ![]() ![]() | Score particles based on how far outside a box they are |
![]() ![]() ![]() ![]() | Apply a function to the distance to a fixed point |
![]() ![]() ![]() ![]() | Find all nearby pairs by testing all pairs |
![]() ![]() ![]() ![]() | Harmonic function (symmetric about the mean) |
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![]() ![]() ![]() ![]() | Lower bound harmonic function (non-zero when feature < mean) |
![]() ![]() ![]() ![]() | A harmonic score on the distance between two spheres |
![]() ![]() ![]() ![]() | Upper bound harmonic function (non-zero when feature > mean) |
![]() ![]() ![]() ![]() | A harmonic upper bound on the diameter of the span of two spheres |
![]() ![]() ![]() ![]() | A harmonic upper bound on the distance between two spheres |
![]() ![]() ![]() ![]() | A well with harmonic barriers |
![]() ![]() ![]() ![]() | A decorator for helping deal with a hierarchy |
![]() ![]() ![]() ![]() | A simple functor to count the number of particles in a hierarchy |
![]() ![]() ![]() ![]() | Define the type for a type of hierarchy |
![]() ![]() ![]() ![]() | A visitor for traversal of a hierarchy |
![]() ![]() ![]() ![]() | Return 1 if the XYZ is in the bounding box, 0 otherwise |
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![]() ![]() ![]() ![]() | Return 1 if two XYZRs collide |
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![]() ![]() ![]() ![]() | Return the hierarchy leaves under a particle |
![]() ![]() ![]() ![]() | Linear function |
![]() ![]() ![]() ![]() | A simple sampler |
![]() ![]() ![]() ![]() | Score based on the minimum scoring members of a set of restraints |
![]() ![]() ![]() ![]() | A visitor which applies a modifier to each kernel::Particle in a hierarchy |
![]() ![]() ![]() ![]() | A Monte Carlo optimizer |
![]() ![]() ![]() ![]() | A base class for classes which perturb particles |
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![]() ![]() ![]() ![]() | This variant of Monte Carlo uses basis hopping |
![]() ![]() ![]() ![]() | This variant of Monte Carlo that relaxes after each move |
![]() ![]() ![]() ![]() | Keep track of statistics about how particles move |
![]() ![]() ![]() ![]() | Ensure that a set of particles remains connected with one another |
![]() ![]() ![]() ![]() | Find all nearby pairs using the algebra::NearestNeighbor code |
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![]() ![]() ![]() ![]() | A decorator for a particle that is part of a rigid body but not rigid |
![]() ![]() ![]() ![]() | A score on the normalized distance between the surfaces of two spheres |
![]() ![]() ![]() ![]() | Modify a set of continuous variables using a normal distribution |
![]() ![]() ![]() ![]() | An OpenCubicSpline |
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![]() ![]() ![]() ![]() | Apply a PairFunction to a Pair |
![]() ![]() ![]() ![]() | Applies a PairScore to a Pair |
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![]() ![]() ![]() ![]() | Apply a QuadFunction to a Quad |
![]() ![]() ![]() ![]() | Find all nearby pairs by testing all pairs |
![]() ![]() ![]() ![]() | Applies a QuadScore to a Quad |
![]() ![]() ![]() ![]() | A a decorator for a particle with an associated reference particle |
![]() ![]() ![]() ![]() | Generate pairs to score by applying a Refiner |
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![]() ![]() ![]() ![]() | A decorator for a rigid body |
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![]() ![]() ![]() ![]() | Accelerated computation of the distance between two rigid bodies |
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![]() ![]() ![]() ![]() | A member of a rigid body, it has internal (local) coordinates |
![]() ![]() ![]() ![]() | Modify the transformation of a rigid body |
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![]() ![]() ![]() ![]() | Modify the transformation of a rigid body |
![]() ![]() ![]() ![]() | Umbrella-like restraint for rigid bodies |
![]() ![]() ![]() ![]() | Perform more efficient close pair finding when rigid bodies are involved |
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![]() ![]() ![]() ![]() | Applies a list of movers one at a time |
![]() ![]() ![]() ![]() | Apply a SingletonFunction to a Singleton |
![]() ![]() ![]() ![]() | Applies a SingletonScore to a Singleton |
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![]() ![]() ![]() ![]() | A score on the distance between the surfaces of two spheres |
![]() ![]() ![]() ![]() | Apply a function to the distance to a fixed point |
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![]() ![]() ![]() ![]() | A simple steepest descent optimizer |
![]() ![]() ![]() ![]() | A lookup based particle refiner |
![]() ![]() ![]() ![]() | Apply a transformation to a passed particle |
![]() ![]() ![]() ![]() | Set the coordinates of a particle to be a transformed version of a reference |
![]() ![]() ![]() ![]() | Set the coordinates of a particle to be a transformed version of a reference |
![]() ![]() ![]() ![]() | Apply a function to the distance between two particles after transforming the first |
![]() ![]() ![]() ![]() | Apply a TripletFunction to a Triplet |
![]() ![]() ![]() ![]() | Applies a TripletScore to a Triplet |
![]() ![]() ![]() ![]() | A function that is harmonic over an interval |
![]() ![]() ![]() ![]() | A decorator for classifying particles in your system |
![]() ![]() ![]() ![]() | Delegate to another PairScore depending on particle types |
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![]() ![]() ![]() ![]() | A restraint that prevents spheres from inter-penetrating |
![]() ![]() ![]() ![]() | Copy the derivatives from a coarse particle to its refined particles |
![]() ![]() ![]() ![]() | A score on a weighted distance between the surfaces of two spheres |
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![]() ![]() ![]() ![]() | A decorator for a particle with x,y,z coordinates |
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![]() ![]() ![]() ![]() | A decorator for a particle with x,y,z coordinates and a radius |
![]() ![]() ![]() ![]() | Display an IMP::core::XYZR particle as a ball |
![]() ![]() ![]() ![]() | Display an IMP::SingletonContainer of IMP::core::XYZR particles as balls |
![]() ![]() ![]() | Output IMP model data in various file formats |
![]() ![]() ![]() ![]() | Display a bounding box |
![]() ![]() ![]() ![]() | Write geometry to a Python file for Chimera to read |
![]() ![]() ![]() ![]() | Represent an RGB color |
![]() ![]() ![]() ![]() | A particle with a color |
![]() ![]() ![]() ![]() | Display a cylinder |
![]() ![]() ![]() ![]() | Display a ellipsoid |
![]() ![]() ![]() ![]() | Remove geometry which is not above a plane |
![]() ![]() ![]() ![]() | The base class for geometry |
![]() ![]() ![]() ![]() | Provide a standard geometry processing framework |
![]() ![]() ![]() ![]() | Group of set of geometric elements |
![]() ![]() ![]() ![]() | Display an isosurface of a density map |
![]() ![]() ![]() ![]() | A text label for a ball in space |
![]() ![]() ![]() ![]() | A base class for geometry contained in particles |
![]() ![]() ![]() ![]() | A base class for geometry from a set of particles |
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![]() ![]() ![]() ![]() | Display a plane as truncated to a bounding box |
![]() ![]() ![]() ![]() | Display a point |
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![]() ![]() ![]() ![]() | Write a CGO file with the geometry |
![]() ![]() ![]() ![]() | Display a reference frame |
![]() ![]() ![]() ![]() | Try to draw some stuff for a generic restraint |
![]() ![]() ![]() ![]() | Geometry for a whole set of restraints |
![]() ![]() ![]() ![]() | Display a segment |
![]() ![]() ![]() ![]() | A base class for geometry contained in particles |
![]() ![]() ![]() ![]() | A base class for geometry from a set of particles |
![]() ![]() ![]() ![]() | Display an isosurface of a density map |
![]() ![]() ![]() ![]() | Display a sphere |
![]() ![]() ![]() ![]() | Display a surface mesh |
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![]() ![]() ![]() ![]() | Display a triangle |
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![]() ![]() ![]() ![]() | Base class for writing geometry to a file |
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![]() ![]() ![]() | Divide-and-conquer inferential optimization in discrete space |
![]() ![]() ![]() ![]() | Store a configuration of a subset |
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![]() ![]() ![]() ![]() | Sample best solutions using BranchAndBound |
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![]() ![]() ![]() ![]() | Add a dependency to the dependency graph |
![]() ![]() ![]() ![]() | A base class for discrete samplers in Domino2 |
![]() ![]() ![]() ![]() | A base class |
![]() ![]() ![]() ![]() | Sample best solutions using Domino |
![]() ![]() ![]() ![]() | Do not allow two particles to be in the same state |
![]() ![]() ![]() ![]() | Define sets of equivalent and exclusive particles |
![]() ![]() ![]() ![]() | Define sets of equivalent particles |
![]() ![]() ![]() ![]() | Do not allow two particles to be in the same state |
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![]() ![]() ![]() ![]() | Maintain an explicit list of what states each particle is allowed to have |
![]() ![]() ![]() ![]() | Filter a configuration of the subset using the kernel::Model thresholds |
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![]() ![]() ![]() ![]() | Store a persistent ordering for a subset based on the list |
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![]() ![]() ![]() ![]() | Filter a configuration of the subset using the kernel::Model thresholds |
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![]() ![]() ![]() ![]() | Store a subset of a subset or assignment |
![]() ![]() ![]() ![]() | Represent a subset of the particles being optimized |
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![]() ![]() ![]() | Basic utilities for handling cryo-electron microscopy 3D density maps |
![]() ![]() ![]() ![]() | Responsible for performing coarse fitting between two density objects |
![]() ![]() ![]() ![]() | Cross correlation coefficient calculator |
![]() ![]() ![]() ![]() | Convolutes two grids |
![]() ![]() ![]() ![]() | Calculate score based on fit to EM map |
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![]() ![]() ![]() ![]() | Class for handling density maps |
![]() ![]() ![]() ![]() | Calculates and stores a distance mask |
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![]() ![]() ![]() ![]() | A restraint for envelope-based scoring of particles in the density map |
![]() ![]() ![]() ![]() | Calculate score based on fit to EM map |
![]() ![]() ![]() ![]() | Class for envelope based scoring using MapDistanceTransform |
![]() ![]() ![]() ![]() | Calculate score based on fit to EM map |
![]() ![]() ![]() ![]() | A simple list of fitting solutions |
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![]() ![]() ![]() ![]() | Class to deal with the header of Electron Microscopy images in IMP |
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![]() ![]() ![]() ![]() | Class for getting the distance from the map envelope |
![]() ![]() ![]() ![]() | The base class to handle reading and writing of density maps |
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![]() ![]() ![]() ![]() | Calculate score based on fit to EM map |
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![]() ![]() ![]() ![]() | Calculates kernel parameters as a function of a specific radius |
![]() ![]() ![]() ![]() | Class for sampling a density map from particles |
![]() ![]() ![]() ![]() | Header for Spider images. IMP-EM is designed to be compatible with it |
![]() ![]() ![]() ![]() | Class to read EM maps (3D) in Spider and Xmipp formats |
![]() ![]() ![]() ![]() | The class represents a molecule as shells of distance from the surface |
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![]() ![]() ![]() | Restraints using electron microscopy 2D images (class averages) |
![]() ![]() ![]() ![]() | Utility functions to extract min/max from the inputs |
![]() ![]() ![]() ![]() | Utility functions to handle cross links |
![]() ![]() ![]() ![]() ![]() | Compute the order of the docking experiments |
![]() ![]() ![]() ![]() ![]() | Puts two subunits together using the Xlinkins restraints |
![]() ![]() ![]() ![]() ![]() | Class defining a cross-link |
![]() ![]() ![]() ![]() ![]() | Description of crosslinking restraints as a python dictionary |
![]() ![]() ![]() ![]() | Utility functions to handle CSV files |
![]() ![]() ![]() ![]() | Utility functions to manage SQL databases with sqlite3 |
![]() ![]() ![]() ![]() ![]() | Class to manage a SQL database built with sqlite3 |
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![]() ![]() ![]() ![]() ![]() | Management of a model using DOMINO |
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![]() ![]() ![]() ![]() ![]() | Class to do Monte Carlo sampling by using as the set of movements relative positions between rigid bodies |
![]() ![]() ![]() ![]() | Utility functions to handle restraints |
![]() ![]() ![]() ![]() | Utility functions to store and retrieve solution information |
![]() ![]() ![]() ![]() ![]() | Simple named tuple class |
![]() ![]() ![]() ![]() ![]() | The heapq algorithm is a min-heap |
![]() ![]() ![]() ![]() ![]() | Class for managing the results of the experiments |
![]() ![]() ![]() ![]() | Functor for hierarchical clustering based on average-linkage |
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![]() ![]() ![]() ![]() | Score based on Chi^2 = ((pixels_image - pixels_projection)/stddev_image)^2 |
![]() ![]() ![]() ![]() | A class to store the clusters generated during hierarchical clustering |
![]() ![]() ![]() ![]() | Determine the collision cross section for some projections of particles |
![]() ![]() ![]() ![]() | Functor for hierarchical clustering based on complete linkage |
![]() ![]() ![]() ![]() | SubsetFilter for checking overlap between projections and images |
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![]() ![]() ![]() ![]() | Dummy restraint between two particles |
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![]() ![]() ![]() ![]() | Parameters used by Em2DRestraint and ProjectionFinder |
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![]() ![]() ![]() ![]() | Comparison by value of the ccc |
![]() ![]() ![]() ![]() | Compare two classes that return a score |
![]() ![]() ![]() ![]() | 2D Electron Microscopy images in IMP |
![]() ![]() ![]() ![]() | Virtual class for reader/writers of images |
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![]() ![]() ![]() ![]() | Class to read and write EM images in JPG format |
![]() ![]() ![]() ![]() | Comparison of pairs by checking the second element |
![]() ![]() ![]() ![]() | Management of projection masks |
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![]() ![]() ![]() ![]() | Score based on the mean of the absolute difference |
![]() ![]() ![]() ![]() | Dummy restraint for a set of particles. Same use as DummyRestraint |
![]() ![]() ![]() ![]() | A restraint for fast scoring of Particles vs. em2d class averages |
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![]() ![]() ![]() ![]() | Parameters given as options to the get_projections() functions |
![]() ![]() ![]() ![]() | Parameters needed for the core projection routine |
![]() ![]() ![]() ![]() | Class to perform registration of model projections to images |
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![]() ![]() ![]() ![]() | Class to manage registration results |
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![]() ![]() ![]() ![]() | Fit rigid bodies to an image |
![]() ![]() ![]() ![]() | Base class for all scoring functions related to em2d |
![]() ![]() ![]() ![]() | Class to provide all the parameters to the segmentation function |
![]() ![]() ![]() ![]() | Functor for hierarchical clustering based on single linkage |
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![]() ![]() ![]() ![]() | Management of reading/writing TIFF images |
![]() ![]() ![]() | Example module |
![]() ![]() ![]() ![]() | Restrain the diameter of a set of points |
![]() ![]() ![]() ![]() | A trivial constraint that just increments a counter |
![]() ![]() ![]() ![]() | A simple decorator which adds a name to a particle |
![]() ![]() ![]() ![]() | An example simple object which is reference counted |
![]() ![]() ![]() ![]() | Apply a harmonic to the distance between two particles |
![]() ![]() ![]() ![]() | Restrain a particle to be in the x,y plane |
![]() ![]() ![]() ![]() | An example singleton modifer |
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![]() ![]() ![]() ![]() | A line segment templated on the dimension |
![]() ![]() ![]() ![]() | A simple unary function |
![]() ![]() ![]() | Several general purpose optimizers from the GNU Scientific Library (GSL) |
![]() ![]() ![]() ![]() | A conjugate gradients optimizer taken from GSL |
![]() ![]() ![]() ![]() | A base class for GSL-based optimizers |
![]() ![]() ![]() ![]() | A quasi-Newton optimizer taken from GSL |
![]() ![]() ![]() ![]() | A simplex optimizer taken from GSL |
![]() ![]() ![]() | Inferential scoring building on methods developed as part of the Inferential Structure Determination software (ISD) |
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![]() ![]() ![]() ![]() ![]() | Class that produces analysis-related output, and is able to parse the output of a file produced by the Statistics class |
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![]() ![]() ![]() ![]() ![]() | Uses column to demux a replica trajectory |
![]() ![]() ![]() ![]() ![]() | Manages information on a given simulation |
![]() ![]() ![]() ![]() | Classes to handle ISD statistics files |
![]() ![]() ![]() ![]() | Classes to store output from replicas |
![]() ![]() ![]() ![]() ![]() | Class that contains the output of one replica, used by the Analysis class |
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![]() ![]() ![]() ![]() ![]() | Nonspecific methods used across all shared function objects |
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![]() ![]() ![]() ![]() ![]() | Statistics gathering and printing class for ISD gibbs sampling |
![]() ![]() ![]() ![]() | Classes to handle TALOS files or folders |
![]() ![]() ![]() ![]() ![]() | Reads a TALOS file, or a TALOS folder, and stores the data |
![]() ![]() ![]() ![]() | Classes to handle TBL files |
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![]() ![]() ![]() ![]() ![]() | When created, estimates the heat capacity from the energies or from the indicator functions using the specified method |
![]() ![]() ![]() ![]() | Miscellaneous utilities |
![]() ![]() ![]() ![]() ![]() | Implements a FIFO pipe that merges lists (see self.put) |
![]() ![]() ![]() ![]() | Ambiguous NOE distance restraint between a number of pairs of particles |
![]() ![]() ![]() ![]() | Apply an ambiguous restraint by computing the d-norm |
![]() ![]() ![]() ![]() | Base class for functions of two variables |
![]() ![]() ![]() ![]() | Covariance function |
![]() ![]() ![]() ![]() | CrossLinkData |
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![]() ![]() ![]() ![]() | CysteineCrossLinkData |
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![]() ![]() ![]() ![]() | FNormal |
![]() ![]() ![]() ![]() | Auxiliary class for FRET_R restraint |
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![]() ![]() ![]() ![]() | GaussianProcessInterpolation |
![]() ![]() ![]() ![]() | Gaussian process restraint |
![]() ![]() ![]() ![]() | Normal probability distribution as a restraint |
![]() ![]() ![]() ![]() | 1D mean function for SAS data |
![]() ![]() ![]() ![]() | Hybrid Monte Carlo optimizer |
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![]() ![]() ![]() ![]() | Linear one-dimensional function |
![]() ![]() ![]() ![]() | Normal probability distribution as a restraint |
![]() ![]() ![]() ![]() | Calculate the -Log of a list of restraints |
![]() ![]() ![]() ![]() | Apply a lognormal distance restraint between two particles |
![]() ![]() ![]() ![]() | Apply an NOE distance restraint between two particles |
![]() ![]() ![]() ![]() | Molecular dynamics optimizer on 1-D and 3-D particles |
![]() ![]() ![]() ![]() | Modify a set of continuous variables using a MD simulation |
![]() ![]() ![]() ![]() | MultivariateFNormalSufficient |
![]() ![]() ![]() ![]() | Apply an NOE distance restraint between two particles |
![]() ![]() ![]() ![]() | Add nuisance parameter to particle |
![]() ![]() ![]() ![]() | A repulsive potential on the distance between two atoms |
![]() ![]() ![]() ![]() | Add scale parameter to particle |
![]() ![]() ![]() ![]() | Add switching parameter to particle |
![]() ![]() ![]() ![]() | Phi/psi dihedral restraint between four particles, using data from TALOS |
![]() ![]() ![]() ![]() | Uniform distribution with harmonic boundaries |
![]() ![]() ![]() ![]() | Base class for functions of one variable |
![]() ![]() ![]() ![]() | VonMises |
![]() ![]() ![]() ![]() | Conjugate prior for the concentration parameter of a von Mises distribution |
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![]() ![]() ![]() ![]() | VonMisesSufficient |
![]() ![]() ![]() ![]() | Add weights for a set of states to a particle |
![]() ![]() ![]() ![]() | Modify the transformation of a rigid body |
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![]() ![]() ![]() | Base functionality and abstract base classes for representation, scoring and sampling |
![]() ![]() ![]() ![]() | Base class for optimizers that act on individual attributes |
![]() ![]() ![]() ![]() | Allow applications to easily implement commmands |
![]() ![]() ![]() ![]() | A class to store a configuration of a model |
![]() ![]() ![]() ![]() | A class to store a set of configurations of a model |
![]() ![]() ![]() ![]() | Implement a constraint on the Model |
![]() ![]() ![]() ![]() | Abstract class for containers of particles |
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![]() ![]() ![]() ![]() | Class for adding derivatives from restraints to the model |
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![]() ![]() ![]() ![]() | A base class for Keys |
![]() ![]() ![]() ![]() | Class for storing model, its restraints, constraints, and particles |
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![]() ![]() ![]() ![]() | Base class for all optimizers |
![]() ![]() ![]() ![]() | Shared optimizer state that is invoked upon commitment of new coordinates |
![]() ![]() ![]() ![]() | IMP-specific subclass of optparse.OptionParser |
![]() ![]() ![]() ![]() | A shared container for Pairs |
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![]() ![]() ![]() ![]() | A base class for modifiers of kernel::ParticlePairsTemp |
![]() ![]() ![]() ![]() | Abstract predicate function |
![]() ![]() ![]() ![]() | Abstract class for scoring object(s) of type ParticlePair |
![]() ![]() ![]() ![]() | Class to handle individual model particles |
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![]() ![]() ![]() ![]() | A shared container for Quads |
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![]() ![]() ![]() ![]() | A base class for modifiers of kernel::ParticleQuadsTemp |
![]() ![]() ![]() ![]() | Abstract predicate function |
![]() ![]() ![]() ![]() | Abstract class for scoring object(s) of type ParticleQuad |
![]() ![]() ![]() ![]() | Abstract class to implement hierarchical methods |
![]() ![]() ![]() ![]() | A restraint is a term in an IMP ScoringFunction |
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![]() ![]() ![]() ![]() | Object used to hold a set of restraints |
![]() ![]() ![]() ![]() | Base class for all samplers |
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![]() ![]() ![]() ![]() | Class for adding up scores during ScoringFunction evaluation |
![]() ![]() ![]() ![]() | ScoreStates maintain invariants in the Model |
![]() ![]() ![]() ![]() | Represents a scoring function on the model |
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![]() ![]() ![]() ![]() | A shared container for Singletons |
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![]() ![]() ![]() ![]() | A base class for modifiers of kernel::ParticlesTemp |
![]() ![]() ![]() ![]() | Abstract predicate function |
![]() ![]() ![]() ![]() | Abstract class for scoring object(s) of type Particle |
![]() ![]() ![]() ![]() | A shared container for Triplets |
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![]() ![]() ![]() ![]() | A base class for modifiers of kernel::ParticleTripletsTemp |
![]() ![]() ![]() ![]() | Abstract predicate function |
![]() ![]() ![]() ![]() | Abstract class for scoring object(s) of type ParticleTriplet |
![]() ![]() ![]() ![]() | Abstract single variable functor class for score functions |
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![]() ![]() ![]() | Functionality for dealing with kinematic mechanical structures |
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![]() ![]() ![]() | Interface to the GPL k-means clustering library |
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![]() ![]() ![]() | Miscellaneous functionality that is not expected to be used by many IMP users |
![]() ![]() ![]() ![]() | Return true for any pair of bonds sharing an endpoint |
![]() ![]() ![]() ![]() | A decorator for a particle with x,y,z coordinates and a radius |
![]() ![]() ![]() ![]() | Maintain a pair container with a decaying list of pairs |
![]() ![]() ![]() ![]() | Track the pairs of particles passed |
![]() ![]() ![]() ![]() | Refine both particles with the refiner and score on the lowest pair |
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![]() ![]() ![]() ![]() | Apply a function to the distance between the cylinders defined by two bonds |
![]() ![]() ![]() ![]() | Allow OptimizerStates to be used as ScoreStates |
![]() ![]() ![]() ![]() | Worm-like-chain energy for polymer chains |
![]() ![]() ![]() | Interface to the Modeller comparative modeling package |
![]() ![]() ![]() ![]() | A single binormal term in a MultipleBinormalRestraint |
![]() ![]() ![]() ![]() | A Modeller restraint which evaluates all defined IMP restraints |
![]() ![]() ![]() ![]() | An IMP restraint using all defined Modeller restraints |
![]() ![]() ![]() ![]() | Read a Modeller model into IMP |
![]() ![]() ![]() ![]() | Modeller-style multiple binormal (phi/psi) restraint |
![]() ![]() ![]() | Template for a module that is stored externally to IMP |
![]() ![]() ![]() | Code that uses the MPI parallel library |
![]() ![]() ![]() ![]() | A class to implement Hamiltonian Replica Exchange |
![]() ![]() ![]() | Fitting atomic structures into a cryo-electron microscopy density map |
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![]() ![]() ![]() ![]() ![]() | Clusters assembly models |
![]() ![]() ![]() ![]() | Storage of anchors (points and edges) |
![]() ![]() ![]() ![]() | Holds data about the assembly density needed for optimization |
![]() ![]() ![]() ![]() | Compute the complementarity between two molecules |
![]() ![]() ![]() ![]() | Holds data about a component needed for optimization |
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![]() ![]() ![]() ![]() | Stores density voxels as a vector of Array1D |
![]() ![]() ![]() ![]() | A simple Restraint that always returns a score of zero |
![]() ![]() ![]() ![]() | An ensemble of fitting solutions |
![]() ![]() ![]() ![]() | Fit a molecule inside its density by local or global FFT |
![]() ![]() ![]() ![]() | Storage of the results from an FFT fit |
![]() ![]() ![]() ![]() | A fitting solution record |
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![]() ![]() ![]() ![]() | Geometric Hash table |
![]() ![]() ![]() ![]() | Utility class for building merge trees |
![]() ![]() ![]() ![]() | Probabilistic anchor graph |
![]() ![]() ![]() ![]() | Stores the anchors sampling space for each protein |
![]() ![]() ![]() ![]() | Storage of proteomics data |
![]() ![]() ![]() ![]() | Align proteomics graph to EM density map |
![]() ![]() ![]() ![]() | Ensure the radius of gyration of particles fits the predicted one |
![]() ![]() ![]() ![]() | Holds header data for optimization |
![]() ![]() ![]() ![]() | Calculate score based on fit to EM map |
![]() ![]() ![]() | Distribute IMP tasks to multiple processors or machines |
![]() ![]() ![]() ![]() | Classes for communicating from the master to slaves |
![]() ![]() ![]() ![]() ![]() | For communicating from the master to slaves |
![]() ![]() ![]() ![]() | Subprocess handling |
![]() ![]() ![]() ![]() | Utilities for the IMP.parallel module |
![]() ![]() ![]() ![]() | A collection of tasks that run in the same environment |
![]() ![]() ![]() ![]() | Base class for all errors specific to the parallel module |
![]() ![]() ![]() ![]() | A slave running on the same machine as the master |
![]() ![]() ![]() ![]() | Manages slaves and contexts |
![]() ![]() ![]() ![]() | Error raised if a problem occurs with the network |
![]() ![]() ![]() ![]() | Error raised if all slaves failed, so tasks cannot be run |
![]() ![]() ![]() ![]() | Error raised if a slave has an unhandled exception |
![]() ![]() ![]() ![]() | An array of slaves in a Sun Grid Engine system parallel environment |
![]() ![]() ![]() ![]() | An array of slaves on a Sun Grid Engine system, started with 'qsub' |
![]() ![]() ![]() ![]() | Representation of a single slave |
![]() ![]() ![]() ![]() | Representation of an array of slaves |
![]() ![]() ![]() | Initial peptide docking |
![]() ![]() ![]() | Python classes to represent, score, sample and analyze models |
![]() ![]() ![]() ![]() | Analysis tools |
![]() ![]() ![]() ![]() ![]() | This class performs alignment and RMSD calculation for two sets of coordinates |
![]() ![]() ![]() ![]() ![]() | A class to cluster structures |
![]() ![]() ![]() ![]() ![]() | A class to compute mean density maps from structures |
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![]() ![]() ![]() ![]() ![]() | Degrees of Freedom Tasks: define rigid bodies and super rigid bodies define symmetries (see representation.py) create nuisances and their parameters generate lists of MC or MD movers |
![]() ![]() ![]() ![]() | Protocols for sampling structures and analyzing them |
![]() ![]() ![]() ![]() ![]() | A macro for running all the basic operations of analysis |
![]() ![]() ![]() ![]() ![]() | This building scheme needs a data structure with the following fields comp_name hier_name color fasta_file fasta_id pdb_name chain_id res_range read_em_files bead_size rb super_rb em_num_components em_txt_file_name em_mrc_file_name |
![]() ![]() ![]() ![]() ![]() | A macro to help setup and run replica exchange, supporting monte carlo and molecular dynamics |
![]() ![]() ![]() ![]() | Nonmaintained code |
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![]() ![]() ![]() ![]() ![]() | This class initialize a CrossLinkMS restraint and contains all useful informations, such as the cross-link database, contained in self.pairs If restraint_file=None, it will proceed creating simulated data |
![]() ![]() ![]() ![]() | Classes for writing output files and processing them |
![]() ![]() ![]() ![]() ![]() | Class for easy writing of PDBs, RMFs, and stat files |
![]() ![]() ![]() ![]() ![]() | A class for reading stat files |
![]() ![]() ![]() ![]() | Representation of the system |
![]() ![]() ![]() ![]() | Sampling of the system |
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![]() ![]() ![]() ![]() ![]() | Useful tools for setting up sampling |
![]() ![]() ![]() ![]() | Miscellaneous utilities |
![]() ![]() ![]() ![]() ![]() | Class to change color code to hexadecimal to rgb |
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![]() ![]() ![]() ![]() | Add resolution to a particle |
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![]() ![]() ![]() ![]() | Add symmetric attribute to a particle |
![]() ![]() ![]() ![]() | Modify the transformation of a rigid body |
![]() ![]() ![]() ![]() | Add Uncertainty to a particle |
![]() ![]() ![]() | Support for the RMF file format for storing hierarchical molecular data and markup |
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![]() ![]() ![]() | Sampling of sidechain rotamers |
![]() ![]() ![]() ![]() | A class storing the rotated coordinates of the atoms in the residue |
![]() ![]() ![]() ![]() | A simple class storing chi angles and their probability |
![]() ![]() ![]() ![]() | A class performing the rotations of atoms in the residues |
![]() ![]() ![]() ![]() | A class storing a whole rotamer library read from a file |
![]() ![]() ![]() | Support for small angle X-ray scattering (SAXS) data |
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![]() ![]() ![]() ![]() | Calculate score based on radius of gyration, taken from saxs profile |
![]() ![]() ![]() ![]() | Calculate score based on fit to SAXS profile |
![]() ![]() ![]() ![]() | Handle the profile for a set of particles, which may include rigid bodies |
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![]() ![]() ![]() | Composable functors to implement scores via compile-time composition |
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![]() ![]() ![]() ![]() | Create efficient distance-based pair scores |
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![]() ![]() ![]() ![]() | Open cubic spline function |
![]() ![]() ![]() ![]() | Orientation-dependent SOAP score |
![]() ![]() ![]() ![]() | A functor for computing a distance based score for two particles |
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![]() ![]() ![]() | A space to add temporary classes while experimenting without forcing you to create your own module |
![]() ![]() ![]() | Code to compute statistical measures |
![]() ![]() ![]() ![]() | Compute the distance between two configurations using chi2 |
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![]() ![]() ![]() ![]() | Embed a configuration using the XYZ coordinates of a set of particles |
![]() ![]() ![]() ![]() | Store data to be clustered for embedding based algorithms |
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![]() ![]() ![]() ![]() | Dynamically build a histogram embedded in D-dimensional space |
![]() ![]() ![]() ![]() | Store data to be clustered for distance metric based algorithms |
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![]() ![]() ![]() ![]() | A base class for clustering results where each item is in one cluster |
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![]() ![]() ![]() ![]() | Simply return the coordinates of a VectorD |
![]() ![]() ![]() | Support for basic symmetry, such as periodic boundary conditions (PBC) |
![]() ![]() ![]() ![]() | Move a particle and keep it in the primitive cell of a periodic lattice |
![]() ![]() ![]() ![]() | Move a rigid body and keep it in the primitive cell of a periodic lattice |
![]() ![]() ![]() | Support for running tests of IMP functionality |
![]() ![]() ![]() ![]() | Super class for simple IMP application test cases |
![]() ![]() ![]() ![]() | Check to make sure the number of director references is as expected |
![]() ![]() ![]() ![]() | Check to make sure the number of C++ object references is as expected |
![]() ![]() ![]() ![]() | Simple RAII-style class to run in a temporary directory |
![]() ![]() ![]() ![]() | Simple RAII-style class to make a temporary directory |
![]() ![]() ![]() ![]() | Super class for IMP test cases |
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