  IMP | Base functionality and abstract base classes for representation, scoring and sampling |
  algebra | General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP modules |
| atom | Functionality for loading, creating, manipulating and scoring atomic structures |
| bayesianem | Restraints for handling electron microscopy maps |
| benchmark | Support for developing and analyzing benchmarks of IMP code |
 bff | Bayesian Fluorescence Framework |
| cli | Tools for handling RMF files |
| restraints | Restraints |
| spectroscopy | Handling of spectroscopy data |
 tools | Utility functions |
| cgal | Make CGAL functionality available to IMP |
| cnmultifit | Generate cyclic atomic structures using cryo-electron microscopy data |
| container | Various classes to hold sets of particles |
| core | Basic functionality that is expected to be used by a wide variety of IMP users |
| display | Output IMP model data in various file formats |
| domino | Divide-and-conquer inferential optimization in discrete space |
| em | Basic utilities for handling cryo-electron microscopy 3D density maps |
| em2d | Restraints using electron microscopy 2D images (class averages) |
| EMageFit | Build assembly models consistent with EM images (class averages) |
| argminmax | Utility functions to extract min/max from the inputs |
| buildxlinks | Utility functions to handle cross links |
| csv_related | Utility functions to handle CSV files |
| database | Utility functions to manage SQL databases with sqlite3 |
| domino_model | Classes to manage a model using DOMINO |
| imp_general | Utility functions that are supposedly not EMageFit-specific |
| alignments | Utility functions to handle alignments |
| comparisons | Utility functions for comparisons |
| io | Utility functions to handle IO |
| movement | Utility functions to handle movement |
| representation | Utility functions to handle representation |
| monte_carlo | Classes for Monte Carlo sampling using rigid body relative moves |
| restraints | Utility functions to handle restraints |
| sampling | Utility functions to handle sampling |
| solutions_io | Utility functions to store and retrieve solution information |
| utility | Utility functions |
| example | Example module |
| foxs | Determine small angle X-ray (SAXS) profiles |
| gsl | Several general purpose optimizers from the GNU Scientific Library (GSL) |
| integrative_docking | Pairwise docking incorporating additional data |
| isd | Inferential scoring building on methods developed as part of the Inferential Structure Determination software (ISD) |
| Entry | Classes to handle ISD statistics files |
| gmm_tools | Tools for handling Gaussian Mixture Models |
| History | Classes to store output from replicas |
| TALOSReader | Classes to handle TALOS files or folders |
| TBLReader | Classes to handle TBL files |
| utils | Miscellaneous utilities |
| kinematics | Functionality for dealing with kinematic mechanical structures |
| kmeans | Interface to the GPL k-means clustering library |
| misc | Miscellaneous functionality that is not expected to be used by many IMP users |
| mmcif | Support for output of models in mmCIF format |
| data | Classes to represent data structures used in mmCIF |
| metadata | Classes to extract metadata for various input files |
| restraint | Map IMP restraints to mmCIF categories |
| util | Utility functions for IMP.mmcif |
| modeller | Interface to the Modeller comparative modeling package |
| mpi | Code that uses the MPI parallel library |
| multi_state | Functionality for handling multi-state models |
| multifit | Fitting atomic structures into a cryo-electron microscopy density map |
| nestor | Nested sampling-based optimization of representation |
| compare_runs_v2_w_pyplot | Plotting script to compare NestOR runs |
| wrapper_v6 | Top-level NestOR script |
| xl_datasplitter | Script to split a CSV file for use in nested sampling |
| npc | Restraints designed for modeling the Nuclear Pore Complex (NPC) |
| npctransport | Simulation of transport through the Nuclear Pore Complex |
| parallel | Distribute IMP tasks to multiple processors or machines |
| manager_communicator | Classes for communicating from the manager to workers |
| subproc | Subprocess handling |
| util | Utilities for the IMP.parallel module |
| pepdock | Initial peptide docking |
| pmi | Python classes to represent, score, sample and analyze models |
| alphabets | Mapping between FASTA one-letter codes and residue types |
| analysis | Tools for clustering and cluster analysis |
| dof | Create movers and set up constraints for PMI objects |
| io | Utility classes and functions for reading and storing PMI files |
| crosslink | Handles cross-link data sets |
| macros | Protocols for sampling structures and analyzing them |
| mmcif | Support for the mmCIF file format |
| output | Classes for writing output files and processing them |
| restraints | Classes to handle different kinds of restraints |
| basic | Some miscellaneous simple restraints |
| crosslinking | Restraints for handling cross-linking data |
| em | Restraints for handling electron microscopy maps |
| em2d | Restraints for handling electron microscopy images |
| npc | Specialized restraints for modeling the Nuclear Pore Complex |
| parameters | Restraints for parameters |
| proteomics | Restraints for handling various kinds of proteomics data |
| saxs | Restraints for handling small angle x-ray (SAXS) data |
| stereochemistry | Restraints for keeping correct stereochemistry |
| samplers | Sampling of the system |
| tools | Miscellaneous utilities |
| topology | Set of Python classes to create a multi-state, multi-resolution IMP hierarchy |
| rmf | Support for the RMF file format for storing hierarchical molecular data and markup |
| rotamer | Sampling of sidechain rotamers |
| sampcon | Sampling exhaustiveness protocol |
| clustering_rmsd | Utilities to cluster and calculate RMSD and precision |
| good_scoring_model_selector | Select good-scoring models based on scores and/or data satisfaction |
| precision_rmsd | Calculation of precision and RMSD |
| rmsd_calculation | Utilities to help with RMSD calculation |
| scores_convergence | Utilities to manage distributions of scores |
| saxs | Support for small angle X-ray scattering (SAXS) data |
| saxs_merge | A method for merging SAXS profiles using Gaussian processes |
| score_functor | Composable functors to implement scores via compile-time composition |
| scratch | A space to add temporary classes while experimenting without forcing you to create your own module |
| spatiotemporal | Spatialtemporal scoring in IMP |
| analysis | Functions to analyze spatiotemporal models |
| composition_scoring | Functions for weighting graphNode objects based on stoichiometry data |
| create_DAG | Simplified function for creating a spatiotemporal model |
| graphNode | Defines the graphNode class |
| prepare_protein_library | Function for preparing spatiotemporal models for sampling |
| score_graph | Functions to traverse and score the spatiotemporal graphs |
| write_output | Functions to write spatiotemporal graph information to files |
| spb | Classes, functions and executables for modeling of the Spindle Pole Body |
| statistics | Code to compute statistical measures |
| symmetry | Support for basic symmetry, such as periodic boundary conditions (PBC) |
| test | Support for running tests of IMP functionality |
| IMP_npctransport | |
