4 This reference guide shows the modules, classes and functions that make
5 up the %IMP API. It is targeted mainly at more advanced users and developers;
6 for an introduction to %IMP, see the [manual](../manual/).
8 To help find things we provide the following indexes:
9 - [Modules](namespaces.html)
10 - [Command line tools](@ref cmdline_tools)
11 - [Methods that create classes](@ref factory_index)
12 - [Methods that use classes](@ref argument_index)
13 - [Which examples each
class is used in](@ref class_example_index)
14 - [Which examples each
function is used in](@ref function_example_index)
16 An overview of some of the various modules currently
17 available. Representative classes and functions are shown. Most
18 modules are licensed under the
20 licensed under the [GPL](http:
21 dependencies. See the doc page
for each module
for details.
23 | Module|Representation|Scoring|Sampling|Analysis|
24 |-------|--------------|-------|--------|--------|
38 | IMP::modeller | | Access to the Modeller scoring functions | | |
Applies a SingletonScore to each Singleton in a list.
display::Geometries create_geometries(RMF::FileConstHandle parent)
Create geometry objects for the geometry nodes found in the file.
PartitionalClusteringWithCenter * create_lloyds_kmeans(Embedding *embedding, unsigned int k, unsigned int iterations)
VectorD< D > get_random_vector_on(const BoundingBoxD< D > &bb)
Generate a random vector on a box with uniform density.
atom::Hierarchies create_hierarchies(RMF::FileConstHandle fh, Model *m)
Apply a function to the angle between three particles.
Restraint * create_restraint(Score *s, const typename Score::Argument &t, std::string name=std::string())
Restraint * create_restraint(Score *s, Container *c, std::string name=std::string())
The base class for geometry.
Calculate score based on fit to SAXS profile.
A voxel grid in d-dimensional space.
Restrain atom pairs based on a set of crosslinks.
Simple conjugate gradients optimizer.
Sample best solutions using Domino.
void write_pdb(const Selection &mhd, TextOutput out, unsigned int model=1)
Return all unordered pairs of particles taken from the SingletonContainer.
Base class for all samplers.
Return all close unordered pairs of particles taken from the SingletonContainer.
void add_hierarchies(RMF::FileHandle fh, const atom::Hierarchies &hs)
Class for storing model, its restraints, constraints, and particles.
Class for handling density maps.
Simple Brownian dynamics simulator.
The standard decorator for manipulating molecular structures.
A Cartesian vector in D-dimensions.
Simple molecular dynamics optimizer.
Store a list of ParticleIndexes.
A simplex optimizer taken from GSL.
A decorator for wrapping a particle representing a molecular bond.
A decorator for a particle representing an atom.
Restraint between two Gaussian Mixture Models, "model" and "density".
PartitionalClustering * create_connectivity_clustering(Metric *metric, double dist)
Base class for all optimizers.
void add_restraints(RMF::FileHandle fh, const Restraints &hs)
A class to store a set of configurations of a model.
A decorator for a particle with x,y,z coordinates.
Hierarchy read_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Read all the molecules in the first model of the PDB file.
Store data to be clustered for embedding based algorithms.
A decorator for a residue.
Represents a scoring function on the model.
double get_rmsd(const core::XYZs &s0, const core::XYZs &s1)
Calculate score based on fit to EM map.
A quasi-Newton optimizer taken from GSL.
Restraints create_restraints(RMF::FileConstHandle fh, Model *m)
Prevent a set of particles and rigid bodies from inter-penetrating.
Class to handle individual particles of a Model object.
Write a CGO file with the geometry.
Store info for a chain of a protein.
A decorator for a rigid body.
void add_geometries(RMF::FileHandle file, const display::GeometriesTemp &r)
Add geometries to the file.
Dynamically build a histogram embedded in D-dimensional space.
A macro to help setup and run replica exchange.
Sample best solutions using BranchAndBound.
Represent a sphere in D-dimensions.
Applies a PairScore to each Pair in a list.
A restraint is a term in an IMP ScoringFunction.
Store data to be clustered for distance metric based algorithms.
A decorator for a particle with x,y,z coordinates and a radius.