Module/Namespace List

Here is a list of all IMP modules - each is also a C++ namespace and a Python package:

[detail level 1234]

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
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
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
pmi1	Legacy PMI1 module to represent, score, sample and analyze models
analysis	Tools for clustering and cluster analysis
io	Utility classes and functions for reading and storing PMI files
crosslink	Handles cross-link data sets
utilities	Utility classes and functions for IO
xltable	Tools to plot a contact map overlaid with cross-links
macros	Protocols for sampling structures and analyzing them
metadata	Classes for attaching metadata to PMI objects
mmcif	Support for the mmCIF file format
nonmaintained	Nonmaintained code
output	Classes for writing output files and processing them
representation	Representation of the system
restraints	Classes to handle different kinds of restraints
basic	Some miscellaneous simple restraints
crosslinking	Restraints for handling crosslinking data
crosslinking_new	Restraints for handling crosslinking 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
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