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IMP Reference Guide  develop.2640aaee5c,2019/11/13
The Integrative Modeling Platform
Module/Namespace List
Here is a list of all IMP modules - each is also a C++ namespace and a Python package:
[detail level 1234]
oNIMPBase functionality and abstract base classes for representation, scoring and sampling
|oNalgebraGeneral purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP modules
|oNatomFunctionality for loading, creating, manipulating and scoring atomic structures
|oNbenchmarkSupport for developing and analyzing benchmarks of IMP code
|oNcgalMake CGAL functionality available to IMP
|oNcnmultifitGenerate cyclic atomic structures using cryo-electron microscopy data
|oNcontainerVarious classes to hold sets of particles
|oNcoreBasic functionality that is expected to be used by a wide variety of IMP users
|oNdisplayOutput IMP model data in various file formats
|oNdominoDivide-and-conquer inferential optimization in discrete space
|oNemBasic utilities for handling cryo-electron microscopy 3D density maps
|oNem2dRestraints using electron microscopy 2D images (class averages)
|oNEMageFitBuild assembly models consistent with EM images (class averages)
||oNargminmaxUtility functions to extract min/max from the inputs
||oNbuildxlinksUtility functions to handle cross links
||oNcsv_relatedUtility functions to handle CSV files
||oNdatabaseUtility functions to manage SQL databases with sqlite3
||oNdomino_modelClasses to manage a model using DOMINO
||oNimp_generalUtility functions that are supposedly not EMageFit-specific
||oNmonte_carloClasses for Monte Carlo sampling using rigid body relative moves
||oNrestraintsUtility functions to handle restraints
||oNsamplingUtility functions to handle sampling
||oNsolutions_ioUtility functions to store and retrieve solution information
||\NutilityUtility functions
|oNexampleExample module
|oNfoxsDetermine small angle X-ray (SAXS) profiles
|oNgslSeveral general purpose optimizers from the GNU Scientific Library (GSL)
|oNintegrative_dockingPairwise docking incorporating additional data
|oNisdInferential scoring building on methods developed as part of the Inferential Structure Determination software (ISD)
||oNEntryClasses to handle ISD statistics files
||oNgmm_toolsTools for handling Gaussian Mixture Models
||oNHistoryClasses to store output from replicas
||oNTALOSReaderClasses to handle TALOS files or folders
||oNTBLReaderClasses to handle TBL files
||\NutilsMiscellaneous utilities
|oNkinematicsFunctionality for dealing with kinematic mechanical structures
|oNkmeansInterface to the GPL k-means clustering library
|oNmiscMiscellaneous functionality that is not expected to be used by many IMP users
|oNmmcifSupport for output of models in mmCIF format
||oNdataClasses to represent data structures used in mmCIF
||oNmetadataClasses to extract metadata for various input files
||oNrestraintMap IMP restraints to mmCIF categories
||\NutilUtility functions for IMP.mmcif
|oNmodellerInterface to the Modeller comparative modeling package
|oNmpiCode that uses the MPI parallel library
|oNmulti_stateFunctionality for handling multi-state models
|oNmultifitFitting atomic structures into a cryo-electron microscopy density map
|oNnpcRestraints designed for modeling the Nuclear Pore Complex (NPC)
|oNnpctransport
|oNparallelDistribute IMP tasks to multiple processors or machines
||oNmaster_communicatorClasses for communicating from the master to slaves
||oNsubprocSubprocess handling
||\NutilUtilities for the IMP.parallel module
|oNpepdockInitial peptide docking
|oNpmiPython classes to represent, score, sample and analyze models
||oNanalysisTools for clustering and cluster analysis
||oNdofCreate movers and set up constraints for PMI objects
||oNioUtility classes and functions for reading and storing PMI files
||oNmacrosProtocols for sampling structures and analyzing them
||oNmmcifSupport for the mmCIF file format
||oNoutputClasses for writing output files and processing them
||oNrestraintsClasses to handle different kinds of restraints
||oNsamplersSampling of the system
||oNtoolsMiscellaneous utilities
||\NtopologySet of Python classes to create a multi-state, multi-resolution IMP hierarchy
|oNpmi1Legacy PMI1 module to represent, score, sample and analyze models
||oNanalysisTools for clustering and cluster analysis
||oNioUtility classes and functions for reading and storing PMI files
||oNmacrosProtocols for sampling structures and analyzing them
||oNmetadataClasses for attaching metadata to PMI objects
||oNmmcifSupport for the mmCIF file format
||oNnonmaintainedNonmaintained code
||oNoutputClasses for writing output files and processing them
||oNrepresentationRepresentation of the system
||oNrestraintsClasses to handle different kinds of restraints
||oNsamplersSampling of the system
||oNtoolsMiscellaneous utilities
||\NtopologySet of python classes to create a multi-state, multi-resolution IMP hierarchy
|oNrmfSupport for the RMF file format for storing hierarchical molecular data and markup
|oNrotamerSampling of sidechain rotamers
|oNsaxsSupport for small angle X-ray scattering (SAXS) data
|oNsaxs_mergeA method for merging SAXS profiles using Gaussian processes
|oNscore_functorComposable functors to implement scores via compile-time composition
|oNscratchA space to add temporary classes while experimenting without forcing you to create your own module
|oNspbClasses, functions and executables for modeling of the Spindle Pole Body
|oNstatisticsCode to compute statistical measures
|oNsymmetrySupport for basic symmetry, such as periodic boundary conditions (PBC)
|\NtestSupport for running tests of IMP functionality
\NIMP_npctransport