IMP Documentation

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:

• Installing IMP
• Introduction
• Tutorial
• Change history
• Modules
• Command line tools
• Biological systems modeled in IMP
• Wiki
• Mailing lists

To help find things we provide the following indexes:

• Methods that create classes
• Methods that use classes
• Which examples each class is used in
• Which examples each function is used in

Additional developer documentation:

• Developers' guide
• Bug Tracker
• Nightly tests

An overview of some of the various modules currently available. Representative classes and functions are shown. Most modules are licensed under the LGPL, however some are licensed under the GPL due to dependencies. See the doc page for each module for details.

Module	Representation	Scoring	Sampling	Analysis
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
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()	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