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IMP Reference Guide  2.7.0
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]
\NIMPBase 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
 ||oNalignmentsUtility functions to handle alignments
 ||oNcomparisonsUtility functions for comparisons
 ||oNioUtility functions to handle IO
 ||oNmovementUtility functions to handle movement
 ||\NrepresentationUtility functions to handle representation
 |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
 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
 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 setup constraints for PMI objects
 |oNioUtility classes and functions for reading and storing PMI files
 ||oNcrosslinkHandles cross-link data sets
 ||oNutilitiesUtility classes and functions for IO
 ||\NxltableTools to plot a contact map overlaid with cross-links
 |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
 ||oNbasicSome miscellaneous simple restraints
 ||oNcrosslinkingRestraints for handling crosslinking data
 ||oNcrosslinking_newRestraints for handling crosslinking data
 ||oNemRestraints for handling electron microscopy maps
 ||oNem2dRestraints for handling electron microscopy images
 ||oNparametersRestraints for parameters
 ||oNproteomicsRestraints for handling various kinds of proteomics data
 ||oNsaxsRestraints for handling small angle x-ray (SAXS) data
 ||\NstereochemistryRestraints for keeping correct stereochemistry
 |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
 oNstatisticsCode to compute statistical measures
 oNsymmetrySupport for basic symmetry, such as periodic boundary conditions (PBC)
 \NtestSupport for running tests of IMP functionality