IMP  2.0.1
The Integrative Modeling Platform
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:

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.

ModuleRepresentationScoringSamplingAnalysis
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