IMP  2.3.1
The Integrative Modeling Platform
mainpage.md
1 Welcome to the IMP library documentation.
2  Throughout the documentation we refer to two, overlapping sets of people.
3 - _users_ write Python scripts to use existing IMP functionality
4 - _developers_ develop new methods for scoring, sampling or representation,
5  and hopefully contribute them back to IMP central.
6  Various pieces of documentation are marked as being intended for developers.
7 
8 In addition to the tabs above that take you to individual module, class and function documentation, we have the following pages to help users get started:
9 - [Installing IMP](@ref installation)
10 - [Introduction](@ref introduction)
11 - [Tutorial](../tutorial/index.html)
12 - [Change history](@ref changelog)
13 - [Modules](namespaces.html)
14 - [Applications](@ref applications)
15 - [Biological systems modeled in IMP](http://integrativemodeling.org/systems/)
16 - [Wiki](https://github.com/salilab/imp/wiki)
17 - [Mailing lists](http://integrativemodeling.org/contact.html)
18 
19 To help find things we provide the following indexes:
20 - [Methods that create classes](@ref factory_index)
21 - [Methods that use classes](@ref argument_index)
22 - [Which examples each class is used in](@ref class_example_index)
23 - [Which examples each function is used in](@ref function_example_index)
24 
25 Additional developer documentation:
26 - [Developers' guide](@ref devguide)
27 - [Bug Tracker](https://github.com/salilab/imp/issues)
28 - [Nightly tests](http://integrativemodeling.org/nightly/results/)
29 
30 An overview of some of the various modules currently
31 available. Representative classes and functions are shown. Most
32 modules are licensed under the
33 [LGPL](http://www.gnu.org/licenses/lgpl.html), however some are
34 licensed under the [GPL](http://www.gnu.org/copyleft/gpl.html) due to
35 dependencies. See the doc page for each module for details.
36 
37 | Module|Representation|Scoring|Sampling|Analysis|
38 |-------|--------------|-------|--------|--------|
39 | IMP::kernel | IMP::kernel::Particle, IMP::kernel::Model | IMP::kernel::Restraint, IMP::kernel::ScoringFunction, IMP::kernel::create_restraint() | IMP::kernel::Optimizer, IMP::kernel::Sampler | IMP::kernel::ConfigurationSet |
40 | IMP::algebra | IMP::algebra::VectorD, IMP::algebra::SphereD, IMP::algebra::GridD, IMP::algebra::Transformation3D... | | IMP::algebra::get_random_vector_on() | |
41 |IMP::statistics | IMP::statistics::Embedding, IMP::statistics::Metric | | | IMP::statistics::create_lloyds_kmeans(), IMP::statistics::create_connectivity_clustering(), IMP::statistics::HistogramD,... |
42 | IMP::display | IMP::display::Geometry | | | IMP::display::PymolWriter, IMP::display::WriteOptimizerState... |
43 | IMP::core | IMP::core::XYZ, IMP::core::XYZR, IMP::core::RigidBody | IMP::core::DistancePairScore, IMP::core::ExcludedVolumeRestraint, IMP::core::AngleTripletScore and other scoring based on distances, angles, volume | IMP::core::MonteCarlo, IMP::core::ConjugateGradients | |
44 | IMP::atom | IMP::atom::Hierarchy, IMP::atom::Atom, IMP::atom::Residue, IMP::atom::Chain, IMP::atom::Bond, IMP::atom::read_pdb() | [charmm_forcefield.py](atom_2charmm_forcefield_8py-example.html) | IMP::atom::BrownianDynamics, IMP::atom::MolecularDynamics | IMP::atom::write_pdb(), IMP::atom::get_rmsd() |
45 |IMP::container | | IMP::container::SingletonsRestraint, IMP::container::PairsRestraint, IMP::container::ListSingletonContainer, IMP::container::ClosePairContainer, IMP::container::AllPairContainer, IMP::container::create_restraint(),...| | |
46 | IMP::rmf | IMP::rmf::create_restraints(), IMP::rmf::create_hierarchies(), IMP::rmf::create_geometries() | | | IMP::rmf::add_restraints(), IMP::rmf::add_hierarchies(), IMP::rmf::add_geometries() |
47 | IMP::em | IMP::em::DensityMap | IMP::em::FitRestraint | | |
48 | IMP::em2d | | IMP::em2d::Em2DRestraint | | |
49 | IMP::saxs | IMP::saxs::Profile | IMP::saxs::Restraint | | |
50 | IMP::gsl | | | IMP::gsl::Simplex, IMP::gsl::QuasiNewton | |
51 | IMP::domino | | | IMP::domino::DominoSampler, IMP::domino::BranchAndBoundSampler | |
52 | IMP::modeller | | Access to the Modeller scoring functions | | |