IMP::pmi Namespace Reference

Python classes to represent, score, sample and analyze models. More...

Detailed Description

Python classes to represent, score, sample and analyze models.

The intention of this module is to provide a variety of high-level Python classes to simplify the construction of a modeling protocol in IMP. One recent use of PMI is the modeling of the Nup84 subcomplex of the nuclear pore complex. Several other applications can be seen at the IMP systems page.

This module is still under heavy development, and should be considered experimental.

See also the PMI changelog.

Author(s): Riccardo Pellarin, Charles Greenberg, Daniel Saltzberg, Peter Cimermancic, Ben Webb, Daniel Russel, Elina Tjioe, Seung Joong Kim, Max Bonomi, Yannick Spill

Maintainer: Riccardo Pellarin

License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Publications:

• See main IMP papers list.

Namespaces
	analysis
	Tools for clustering and cluster analysis.
	dof
	Setup constraints and create movers for an IMP Hierarchy.
	io
	Utility classes and functions for reading and storing PMI files.
	macros
	Protocols for sampling structures and analyzing them.
	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.
	samplers
	Sampling of the system.
	sampling_tools
	Useful tools for setting up sampling.
	tools
	Miscellaneous utilities.
	topology
	Set up of system representation from topology files.

Classes
class	CompositeRestraint
	A restraint for ambiguous cross-linking MS data and multiple state approach. More...
class	Resolution
	Add resolution to a particle. More...
class	SigmoidRestraintSphere
	Simple sigmoidal score calculated between sphere surfaces. More...
class	Symmetric
	Add symmetric attribute to a particle. More...
class	TransformMover
	Modify the transformation of a rigid body. More...
class	Uncertainty
	Add uncertainty to a particle. More...

Functions
RestraintSet *	create_elastic_network (const Particles &ps, Float dist_cutoff, Float strength)
	Create an elastic network restraint set. More...
Float	get_bipartite_minimum_sphere_distance (const IMP::core::XYZRs &m1, const IMP::core::XYZRs &m2)
Floats	get_list_of_bipartite_minimum_sphere_distance (const ParticlesTemps &pss)

Standard module functions
All IMP modules have a set of standard functions to help get information about the module and about files associated with the module.
std::string	get_module_version ()
std::string	get_module_name ()
std::string	get_data_path (std::string file_name)
	Return the full path to one of this module's data files. More...
std::string	get_example_path (std::string file_name)
	Return the full path to one of this module's example files. More...

Function Documentation

RestraintSet* IMP::pmi::create_elastic_network	(	const Particles &	ps,
		Float	dist_cutoff,
		Float	strength
	)

Create an elastic network restraint set.

Definition at line 20 of file utilities.h.

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std::string IMP::pmi::get_data_path

(

std::string

file_name

)

Return the full path to one of this module's data files.

To read the data file "data_library" that was placed in the data directory of this module, do something like

std::ifstream in(IMP::pmi::get_data_path("data_library"));

This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.

Note

Each module has its own data directory, so be sure to use this function from the correct module.

std::string IMP::pmi::get_example_path

(

std::string

file_name

)

Return the full path to one of this module's example files.

To read the example file "example_protein.pdb" that was placed in the examples directory of this module, do something like

std::ifstream in(IMP::pmi::get_example_path("example_protein.pdb"));

This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.

Note

Each module has its own example directory, so be sure to use this function from the correct module.