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.
An overview of the various modules currently available. Representative classes and functions are shown.
| Module | Representation | Scoring | Sampling | Analysis |
| IMP | IMP::Particle | IMP::Restraint | IMP::Optimizer, IMP::Sampler | IMP::write_particles(), IMP::read_particles(), IMP::write_particles_binary(), IMP::read_particles_binary() |
| 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::MCCGSampler, 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()... | Charmm force-field based scoring | IMP::atom::BrownianDynamics, IMP::atom::MolecularDynamics | IMP::atom::write_pdb() |
| IMP::container | | IMP::container::SingletonsRestraint, IMP::container::PairsRestraint, IMP::container::ListSingletonContainer, IMP::container::ClosePairContainer, IMP::container::AllPairContainer... | | |
| IMP::statistics | | | | IMP::statistics::get_lloyds_kmeans(), IMP::statistics::get_connectivity_clustering() |
| IMP::em | | IMP::em::FitRestraint | | |
| IMP::em2d | | IMP::em2d::Em2DRestraint | | |
| IMP::saxs | | IMP::saxs::Restraint | | |
| IMP::gsl | | | IMP::gsl::Simplex, IMP::gsl::QuasiNewton | |
| IMP::domino | | | | IMP::domino::DominoSampler, IMP::domino::BranchAndBoundSampler |
| IMP::display | | | | IMP::display::PymolWriter, IMP::display::ChimeraWriter, IMP::display::WriteOptimizerState... |
| IMP::restrainer | proteins as rigid bodies or a collection of balls | Yeast-2-hybrid, EM density maps | | |
| IMP::modeller | | Access to the Modeller scoring functions | | |
Not listed are
- IMP::algebra that provides basic geometric and mathematical types and operations
- IMP::benchmark that provides benchmarks of various usages of other modules
