Welcome to the IMP
library documentation. Throughout the documentation we refer to two, overlapping sets of people.
- users write python scripts to use existing
IMP
functionality
- developers develop new methods for scoring, sampling or representation, and hopefully contribute them back to
IMP
central Various pieces of documentation are marked as being intended for developers.
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:
To help find things we provide the following indexes:
Additional developer documentation:
An overview of the various modules currently available. Representative classes and functions are shown.
Module | Representation | Scoring | Sampling | Analysis |
IMP.kernel | IMP::Particle, IMP::Model | IMP::Restraint, IMP::ScoringFunction, IMP::create_restraint() | IMP::Optimizer, IMP::Sampler | IMP::ConfigurationSet |
IMP::algebra | IMP::algebra::VectorD, IMP::algebra::SphereD, IMP::algebra::GridD, IMP::algebra::Transformation3D... | | IMP::algebra::get_random_vector_on() | |
IMP::statistics | IMP::statistics::Embedding, IMP::statistics::Metric | | | IMP::statistics::create_lloyds_kmeans(), IMP::statistics::create_connectivity_clustering(), IMP::statistics::HistogramD,... |
IMP::display | IMP::display::Geometry | | | IMP::display::PymolWriter, IMP::display::WriteOptimizerState... |
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 | |
IMP::atom | IMP::atom::Hierarchy, IMP::atom::Atom, IMP::atom::Residue, IMP::atom::Chain, IMP::atom::Bond, IMP::atom::read_pdb()... | examples/atom/charmm_forcefield.py | IMP::atom::BrownianDynamics, IMP::atom::MolecularDynamics | IMP::atom::write_pdb(), IMP::atom::get_rmsd() |
IMP::container | | IMP::container::SingletonsRestraint, IMP::container::PairsRestraint, IMP::container::ListSingletonContainer, IMP::container::ClosePairContainer, IMP::container::AllPairContainer, IMP::container::create_restraint(),... | | |
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() |
IMP::em | IMP::em::DensityMap | IMP::em::FitRestraint | | |
IMP::em2d | | IMP::em2d::Em2DRestraint | | |
IMP::saxs | IMP::saxs::Profile | IMP::saxs::Restraint | | |
IMP::gsl | | | IMP::gsl::Simplex, IMP::gsl::QuasiNewton | |
IMP::domino | | | IMP::domino::DominoSampler, IMP::domino::BranchAndBoundSampler | |
IMP::modeller | | Access to the Modeller scoring functions | | |